Variant report

Variant	rs4925109
Chromosome Location	chr17:17661802-17661803
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:0)
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	chr17:17661730..17664438-chr17:17712426..17715101,2	MCF-7	breast:
2	chr17:17655972..17658628-chr17:17659930..17661835,2	K562	blood:
3	chr17:17653860..17663088-chr17:17683787..17689208,13	MCF-7	breast:
4	chr17:17661411..17663516-chr3:161089325..161091163,2	MCF-7	breast:
5	chr17:17632855..17634873-chr17:17660270..17661938,2	MCF-7	breast:
6	chr17:17661516..17664034-chr17:17666915..17668901,2	MCF-7	breast:
7	chr17:17659679..17662108-chr17:17664180..17666491,2	K562	blood:
8	chr17:17653399..17659141-chr17:17659467..17667043,10	MCF-7	breast:
9	chr17:17623843..17637985-chr17:17653006..17664308,33	MCF-7	breast:
10	chr17:17597397..17599561-chr17:17661548..17663067,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11649804	0.81[GIH][hapmap]
rs11655029	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11656775	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12940014	0.86[JPT][hapmap]
rs12945601	0.86[CEU][hapmap]
rs4925104	0.85[JPT][hapmap]
rs4925108	0.86[CEU][hapmap]
rs4925114	0.90[GIH][hapmap]
rs7224617	0.86[JPT][hapmap]
rs752579	0.90[CEU][hapmap]
rs8067439	0.81[GIH][hapmap]
rs941448	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9900803	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4925109	TOM1L2	cis	cerebellum	SCAN
rs4925109	TOM1L2	cis	parietal	SCAN
rs4925109	SHMT1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17651600-17663600	Enhancers	Fetal Heart	heart
2	chr17:17656600-17662400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:17656600-17665600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:17656600-17682200	Weak transcription	Small Intestine	intestine
5	chr17:17656800-17668800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:17656800-17669800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr17:17656800-17669800	Weak transcription	Colonic Mucosa	Colon
8	chr17:17657000-17663600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr17:17657000-17666200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:17657000-17666400	Weak transcription	Adipose Nuclei	Adipose
11	chr17:17657000-17670400	Weak transcription	NH-A	brain
12	chr17:17657000-17677400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr17:17657200-17662600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:17657200-17664400	Weak transcription	HepG2	liver
15	chr17:17657200-17669600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr17:17657200-17675200	Weak transcription	Osteobl	bone
17	chr17:17657400-17662800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:17657400-17662800	Weak transcription	HMEC	breast
19	chr17:17657400-17664200	Strong transcription	Dnd41	blood
20	chr17:17657400-17666400	Weak transcription	HSMMtube	muscle
21	chr17:17657400-17666800	Weak transcription	HSMM	muscle
22	chr17:17657400-17667200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:17657400-17668600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:17657400-17668800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr17:17657400-17671000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr17:17657800-17664000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:17658200-17664000	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr17:17658400-17663000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr17:17658800-17664600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:17658800-17668800	Weak transcription	Brain Substantia Nigra	brain
31	chr17:17659000-17662200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr17:17659000-17662400	Weak transcription	Esophagus	oesophagus
33	chr17:17659000-17662400	Enhancers	Spleen	Spleen
34	chr17:17659000-17664600	Weak transcription	Liver	Liver
35	chr17:17659000-17664800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr17:17659000-17667600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:17659200-17662600	Enhancers	Primary B cells from peripheral blood	blood
38	chr17:17659200-17663800	Weak transcription	Placenta	Placenta
39	chr17:17659400-17662400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr17:17659400-17663600	Weak transcription	Lung	lung
41	chr17:17659400-17665200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:17659400-17666600	Weak transcription	A549	lung
43	chr17:17659800-17662000	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr17:17659800-17664000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr17:17660000-17662000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr17:17660000-17663600	Enhancers	Brain Anterior Caudate	brain
47	chr17:17660000-17665400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr17:17660000-17667000	Genic enhancers	Fetal Intestine Small	intestine
49	chr17:17660200-17662000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:17660200-17662000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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