Variant report

Variant	rs11868035
Chromosome Location	chr17:17715101-17715102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17685362..17690405-chr17:17711256..17718354,8	MCF-7	breast:
2	chr17:17583537..17586679-chr17:17711908..17715201,3	MCF-7	breast:
3	chr17:17709472..17711211-chr17:17713888..17716285,2	MCF-7	breast:
4	chr17:17683398..17686891-chr17:17713626..17715555,3	K562	blood:
5	chr17:17713571..17716045-chr17:17763019..17766158,3	K562	blood:
6	chr17:17588552..17591494-chr17:17713453..17715244,2	MCF-7	breast:
7	chr17:17583640..17587401-chr17:17713270..17717474,6	MCF-7	breast:
8	chr17:17715002..17715792-chr17:17763094..17764226,6	MCF-7	breast:
9	chr17:17583267..17586800-chr17:17714001..17718221,4	K562	blood:
10	chr17:17655283..17657640-chr17:17714232..17716062,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMCR5-3	chr17:17714665-17715370	NONHSAT146109

No data

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction
ENSG00000175662	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11649804	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11654081	0.84[CEU][hapmap]
rs11656665	0.82[CEU][hapmap]
rs12453837	0.97[ASN][1000 genomes]
rs12946913	0.93[ASN][1000 genomes]
rs16960744	0.83[JPT][hapmap]
rs2297508	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2350976	0.82[CEU][hapmap]
rs3803763	0.90[EUR][1000 genomes]
rs4925114	0.86[CEU][hapmap]
rs4925115	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4925119	0.82[JPT][hapmap]
rs4925120	0.83[JPT][hapmap]
rs8066560	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs8067439	0.80[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv907753	chr17:17573539-17747289	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv907754	chr17:17573539-17782404	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
8	nsv1061126	chr17:17578826-17803194	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv543238	chr17:17578826-17803194	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv833385	chr17:17594037-17765578	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
11	nsv1058884	chr17:17594370-17803194	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
12	nsv543240	chr17:17594370-17803194	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
13	nsv1064176	chr17:17596222-17803194	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv543242	chr17:17596222-17803194	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
15	nsv1062361	chr17:17598407-17746899	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv543243	chr17:17598407-17746899	Genic enhancers Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
17	nsv907756	chr17:17619859-17747289	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
18	nsv522668	chr17:17619859-17752809	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
19	nsv907757	chr17:17619859-17752809	Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
20	nsv907758	chr17:17619859-17782404	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
21	nsv907759	chr17:17619859-17802478	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
22	nsv1059949	chr17:17632590-17803194	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
23	nsv543244	chr17:17632590-17803194	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
24	nsv907760	chr17:17649423-17782404	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
25	nsv907761	chr17:17649423-17802478	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
26	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
27	nsv907762	chr17:17668071-17802478	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
28	nsv907763	chr17:17673824-17749822	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
29	nsv907764	chr17:17673824-17754633	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
30	nsv907765	chr17:17682484-17802478	Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
31	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
32	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
33	nsv526904	chr17:17696755-17715101	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	nsv817753	chr17:17696755-17715101	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
35	nsv907767	chr17:17709136-17733760	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
36	nsv907768	chr17:17709136-17747289	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Parkinson's disease	21738487	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11868035	TOM1L2	cis	parietal	SCAN
rs11868035	TOM1L2	cis	cerebellum	SCAN
rs11868035	SREBF1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17695400-17723800	Strong transcription	Dnd41	blood
2	chr17:17697200-17715200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:17697200-17715200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:17697200-17715800	Strong transcription	Thymus	Thymus
5	chr17:17697400-17715400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:17707000-17723000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:17707400-17722400	Weak transcription	Primary B cells from cord blood	blood
8	chr17:17708000-17715400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:17708000-17723600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:17708400-17716600	Enhancers	Fetal Heart	heart
11	chr17:17709200-17717800	Weak transcription	Psoas Muscle	Psoas
12	chr17:17709800-17716000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr17:17710000-17721800	Weak transcription	HSMM	muscle
14	chr17:17710200-17724400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:17710400-17715400	Weak transcription	Brain Substantia Nigra	brain
16	chr17:17711800-17721600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr17:17712200-17716000	Enhancers	NH-A	brain
18	chr17:17712200-17716200	Enhancers	Fetal Lung	lung
19	chr17:17712200-17716200	Genic enhancers	Lung	lung
20	chr17:17712600-17715400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr17:17712800-17715400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr17:17712800-17724000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:17713000-17716400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr17:17713200-17715400	Strong transcription	Spleen	Spleen
25	chr17:17713200-17716600	Enhancers	Fetal Brain Male	brain
26	chr17:17713200-17720800	Weak transcription	GM12878-XiMat	blood
27	chr17:17713400-17716000	Genic enhancers	Fetal Thymus	thymus
28	chr17:17713400-17716200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:17713400-17716200	Enhancers	Liver	Liver
30	chr17:17713400-17716400	Genic enhancers	Brain Inferior Temporal Lobe	brain
31	chr17:17713400-17716800	Genic enhancers	Placenta	Placenta
32	chr17:17713400-17721600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:17713400-17722800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr17:17713600-17715200	Strong transcription	Primary T cells from cord blood	blood
35	chr17:17713600-17715400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr17:17713600-17715600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
37	chr17:17713600-17716000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:17713600-17717800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr17:17713600-17721600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr17:17713800-17715400	Genic enhancers	Brain Cingulate Gyrus	brain
41	chr17:17713800-17715600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:17713800-17716000	Genic enhancers	Adipose Nuclei	Adipose
43	chr17:17713800-17716000	Genic enhancers	Fetal Intestine Large	intestine
44	chr17:17713800-17716000	Genic enhancers	Fetal Stomach	stomach
45	chr17:17713800-17716200	Genic enhancers	Colonic Mucosa	Colon
46	chr17:17713800-17716600	Strong transcription	Osteobl	bone
47	chr17:17713800-17716800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:17713800-17720000	Genic enhancers	Fetal Muscle Leg	muscle
49	chr17:17713800-17721200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr17:17714000-17715200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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