Variant report

Variant	rs3767208
Chromosome Location	chr1:70693731-70693732
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:70693167-70693775	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:70693176-70693792	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:70686388-70698918	K562	blood:	n/a	n/a
4	POLR2A	chr1:70693072-70693776	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:70692922-70693950	HepG2	liver:	n/a	n/a
6	CUX1	chr1:70693665-70694071	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70687323..70689346-chr1:70692516..70694332,3	MCF-7	breast:
2	chr1:70684364..70687178-chr1:70692446..70695041,2	MCF-7	breast:

Variant related genes	Relation type
SRSF11	TF binding region
ENSG00000116754	Chromatin interaction
ENSG00000228988	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10489927	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562802	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565362	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131235	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131248	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131251	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2210545	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274913	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297484	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297486	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2478801	0.89[AMR][1000 genomes]
rs34821575	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35262515	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767214	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920731	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41488747	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4649913	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650031	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55727788	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56902977	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58639674	0.86[ASN][1000 genomes]
rs58696538	0.88[EUR][1000 genomes]
rs58927829	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59234513	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60272091	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60441970	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs632517	0.89[AMR][1000 genomes]
rs655588	0.85[AMR][1000 genomes]
rs668525	0.94[AMR][1000 genomes]
rs6702168	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716240	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74085992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085996	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74088004	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088016	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088029	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74088032	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74088035	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088042	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv871898	chr1:70681486-70723347	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1014292	chr1:70689215-70799065	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3767208	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70687800-70697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:70687800-70698600	Weak transcription	Gastric	stomach
3	chr1:70687800-70698800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:70687800-70699600	Weak transcription	Lung	lung
5	chr1:70687800-70699600	Weak transcription	Spleen	Spleen
6	chr1:70688000-70697200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:70688000-70697200	Weak transcription	Pancreas	Pancrea
8	chr1:70688000-70697800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:70688000-70699000	Weak transcription	Psoas Muscle	Psoas
10	chr1:70688000-70710400	Weak transcription	Aorta	Aorta
11	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
12	chr1:70688200-70696200	Weak transcription	Colonic Mucosa	Colon
13	chr1:70688200-70708200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:70688400-70693800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:70688400-70719400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:70688600-70719800	Strong transcription	Fetal Thymus	thymus
17	chr1:70689000-70694800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:70689000-70717800	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr1:70689000-70718200	Strong transcription	Placenta	Placenta
20	chr1:70689200-70697000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:70689200-70718600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:70689400-70694600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:70689400-70719200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:70689600-70694000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:70689600-70694000	Genic enhancers	Dnd41	blood
26	chr1:70689600-70694200	Strong transcription	Fetal Muscle Leg	muscle
27	chr1:70689600-70719200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr1:70689600-70719200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:70689800-70696600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:70689800-70697400	Weak transcription	Fetal Intestine Small	intestine
31	chr1:70690000-70694600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:70690000-70695800	Weak transcription	Brain Substantia Nigra	brain
33	chr1:70690000-70698400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:70690200-70694200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:70690200-70696600	Weak transcription	Fetal Kidney	kidney
36	chr1:70690200-70719800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:70690400-70694000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:70690400-70694200	Weak transcription	Brain Germinal Matrix	brain
39	chr1:70690400-70696600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:70690400-70719800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:70690600-70693800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:70690600-70699400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:70690600-70716000	Weak transcription	Stomach Mucosa	stomach
44	chr1:70690600-70719200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:70690800-70694000	Weak transcription	Fetal Brain Male	brain
46	chr1:70690800-70718200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:70690800-70718600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:70690800-70719200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:70691200-70693800	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr1:70691200-70695200	Strong transcription	Fetal Intestine Large	intestine

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