Variant report

Variant	rs9905702
Chromosome Location	chr17:17633932-17633933
allele	A/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17631993..17634623-chr17:17684416..17687252,2	MCF-7	breast:
2	chr17:17633057..17635019-chr17:17635341..17638302,3	K562	blood:
3	chr17:17591306..17603641-chr17:17622226..17637880,43	MCF-7	breast:
4	chr17:17582718..17591238-chr17:17621630..17636217,47	MCF-7	breast:
5	chr17:17600627..17603876-chr17:17631337..17634332,3	K562	blood:
6	chr17:17630393..17635386-chr17:17740565..17747416,7	MCF-7	breast:
7	chr17:17632292..17634570-chr17:17720118..17721713,2	MCF-7	breast:
8	chr17:17632855..17634873-chr17:17660270..17661938,2	MCF-7	breast:
9	chr17:17631936..17635055-chr17:17641317..17644027,3	K562	blood:
10	chr17:17630976..17634790-chr17:17640021..17644758,7	MCF-7	breast:
11	chr17:17631991..17634660-chr17:17636330..17637889,2	MCF-7	breast:
12	chr17:17623843..17637985-chr17:17653006..17664308,33	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12938840	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12938914	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2001421	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2350962	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2882552	0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4074643	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4244601	0.87[JPT][hapmap]
rs4636969	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924813	0.86[JPT][hapmap]
rs4925103	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4995264	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs720856	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7209595	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7213879	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7225141	0.84[CEU][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs8067800	0.85[EUR][1000 genomes]
rs8071107	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs9899364	0.84[CEU][hapmap]
rs9900148	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9907986	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv543241	chr17:17596222-17703059	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	12 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	nsv532109	chr17:17630064-17700497	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	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
26	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9905702	TOM1L2	cis	parietal	SCAN
rs9905702	LLGL1	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17616200-17642000	Weak transcription	K562	blood
2	chr17:17627800-17642600	Weak transcription	Aorta	Aorta
3	chr17:17628000-17635800	Weak transcription	HSMM	muscle
4	chr17:17628200-17636200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr17:17628400-17636600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:17628800-17634000	Weak transcription	Ovary	ovary
7	chr17:17628800-17641000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr17:17628800-17641200	Weak transcription	Fetal Kidney	kidney
9	chr17:17629200-17636200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:17629400-17636200	Strong transcription	Dnd41	blood
11	chr17:17629600-17641200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr17:17629800-17635400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr17:17629800-17635400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:17629800-17636200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:17629800-17640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:17629800-17642000	Weak transcription	HepG2	liver
17	chr17:17630000-17634600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr17:17630000-17635800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr17:17630000-17638000	Strong transcription	Fetal Intestine Small	intestine
20	chr17:17630000-17639800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:17630000-17641200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr17:17630200-17634000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr17:17630200-17634600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:17630200-17641200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr17:17630400-17634800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr17:17630400-17639600	Weak transcription	Primary B cells from cord blood	blood
27	chr17:17630400-17640800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr17:17630600-17635400	Weak transcription	Primary T cells from cord blood	blood
29	chr17:17630600-17635400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr17:17630600-17637000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:17630600-17641000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr17:17630800-17634400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:17630800-17635000	Enhancers	Esophagus	oesophagus
34	chr17:17630800-17637200	Enhancers	HMEC	breast
35	chr17:17630800-17637600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr17:17630800-17638400	Enhancers	Right Ventricle	heart
37	chr17:17630800-17646000	Enhancers	Fetal Heart	heart
38	chr17:17631000-17637000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:17631000-17637400	Enhancers	Brain Angular Gyrus	brain
40	chr17:17631000-17641400	Weak transcription	HUVEC	blood vessel
41	chr17:17631200-17634000	Enhancers	Placenta	Placenta
42	chr17:17631200-17634200	Enhancers	Gastric	stomach
43	chr17:17631200-17635400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr17:17631400-17634400	Weak transcription	Pancreas	Pancrea
45	chr17:17631400-17634400	Enhancers	Stomach Mucosa	stomach
46	chr17:17631400-17637000	Enhancers	Brain Anterior Caudate	brain
47	chr17:17631400-17642200	Weak transcription	Liver	Liver
48	chr17:17631400-17643600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:17631600-17634600	Enhancers	Brain Hippocampus Middle	brain
50	chr17:17631800-17635000	Enhancers	Brain Germinal Matrix	brain

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