Variant report

Variant	rs709210
Chromosome Location	chr3:50357869-50357870
allele	G/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50324564..50342616-chr3:50350801..50362499,49	MCF-7	breast:
2	chr3:50327926..50342388-chr3:50350886..50359960,36	MCF-7	breast:
3	chr3:50300460..50314689-chr3:50349154..50363682,34	MCF-7	breast:
4	chr3:50357006..50359780-chr3:50383259..50385095,2	MCF-7	breast:
5	chr3:50314390..50316856-chr3:50357107..50359753,2	MCF-7	breast:
6	chr3:50273339..50275012-chr3:50356233..50359158,2	K562	blood:
7	chr3:50295790..50299500-chr3:50356173..50362991,11	MCF-7	breast:
8	chr3:50296091..50300659-chr3:50356103..50362246,11	MCF-7	breast:
9	chr3:50334885..50342502-chr3:50352987..50366859,26	K562	blood:
10	chr3:50307238..50313479-chr3:50353130..50365794,18	MCF-7	breast:
11	chr3:50273482..50276230-chr3:50357348..50359283,2	MCF-7	breast:
12	chr3:50356822..50362778-chr3:50372728..50378128,10	MCF-7	breast:
13	chr3:50315023..50318386-chr3:50356939..50360295,5	MCF-7	breast:
14	chr3:50326497..50331702-chr3:50356299..50362839,8	K562	blood:
15	chr3:50334334..50341950-chr3:50357130..50360296,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000114378	Chromatin interaction
ENSG00000186792	Chromatin interaction
ENSG00000214706	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000243477	Chromatin interaction
ENSG00000004838	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000179564	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000230454	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1076872	1.00[ASW][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap]
rs11917680	0.94[CHD][hapmap];0.84[MEX][hapmap]
rs12637870	0.94[CHD][hapmap]
rs2236989	0.94[CHD][hapmap]
rs2282755	0.94[CHD][hapmap];0.81[JPT][hapmap]
rs41499647	0.94[CHD][hapmap]
rs4547694	0.82[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap]
rs9877046	1.00[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription 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	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription 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	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription 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	104 gene(s)	inside rSNPs	diseases
9	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
10	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription 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	74 gene(s)	inside rSNPs	diseases
11	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
12	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
13	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
14	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers 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	93 gene(s)	inside rSNPs	diseases
16	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	82 gene(s)	inside rSNPs	diseases
17	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	83 gene(s)	inside rSNPs	diseases
18	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers 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	83 gene(s)	inside rSNPs	diseases
19	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
20	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
21	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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 target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs709210	SEMA3G	cis	parietal	SCAN
rs709210	CELSR3	cis	parietal	SCAN
rs709210	RBM6	cis	cerebellum	SCAN
rs709210	PTH1R	cis	parietal	SCAN
rs709210	CCDC71	cis	parietal	SCAN
rs709210	PTH1R	cis	cerebellum	SCAN
rs709210	HYAL3	cis	Esophagus Muscularis	GTEx
rs709210	RNF123	cis	parietal	SCAN
rs709210	HYAL3	cis	Heart Left Ventricle	GTEx
rs709210	HYAL3	cis	Frontal Cortex	GTEx
rs709210	HYAL3	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50352800-50358000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:50353000-50358000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:50353400-50358000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr3:50353400-50358000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:50353800-50358000	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:50354200-50358200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
7	chr3:50355000-50358000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:50355000-50358000	Enhancers	Primary B cells from cord blood	blood
9	chr3:50355600-50358400	Transcr. at gene 5' and 3'	Lung	lung
10	chr3:50355600-50358400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr3:50355800-50358200	Transcr. at gene 5' and 3'	Spleen	Spleen
12	chr3:50356200-50358000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:50356200-50358000	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
14	chr3:50356400-50358000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:50356800-50358000	Enhancers	Primary T cells from cord blood	blood
16	chr3:50356800-50358000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
17	chr3:50357000-50358200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:50357200-50358000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:50357200-50358000	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr3:50357200-50358000	Flanking Active TSS	HepG2	liver
21	chr3:50357200-50358200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:50357200-50358400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr3:50357200-50358400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr3:50357400-50358000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:50357400-50358000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:50357400-50358000	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
27	chr3:50357400-50358000	Enhancers	Fetal Thymus	thymus
28	chr3:50357400-50358000	Transcr. at gene 5' and 3'	Pancreas	Pancrea
29	chr3:50357400-50358000	Flanking Active TSS	Right Atrium	heart
30	chr3:50357400-50358000	Enhancers	Small Intestine	intestine
31	chr3:50357400-50358200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:50357400-50358200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:50357400-50358200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:50357400-50358200	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr3:50357400-50358200	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr3:50357400-50358200	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr3:50357400-50358200	Flanking Active TSS	Esophagus	oesophagus
38	chr3:50357400-50358200	Flanking Active TSS	HMEC	breast
39	chr3:50357400-50358200	Flanking Active TSS	HSMM	muscle
40	chr3:50357400-50358400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:50357400-50358400	Flanking Active TSS	Colonic Mucosa	Colon
42	chr3:50357400-50358400	Flanking Active TSS	Fetal Brain Female	brain
43	chr3:50357400-50358400	Flanking Active TSS	Fetal Heart	heart
44	chr3:50357400-50358400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr3:50357400-50358400	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr3:50357600-50358000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:50357600-50358000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:50357600-50358000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:50357600-50358000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:50357600-50358000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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