Variant report

Variant	rs56902977
Chromosome Location	chr1:70690465-70690466
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:70689784-70691462	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:70690157-70691467	A549	lung:	n/a	n/a
3	POLR2A	chr1:70686388-70698918	K562	blood:	n/a	n/a
4	POLR2A	chr1:70689973-70690677	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:70690427-70690491	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:70690412-70690596	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:70689625-70691541	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:70690385-70690971	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70687235..70688815-chr1:70690103..70691870,2	MCF-7	breast:
2	chr1:70669146..70671967-chr1:70689438..70693050,5	K562	blood:
3	chr1:70688424..70691720-chr1:70692048..70694571,6	MCF-7	breast:
4	chr1:70688440..70690850-chr1:70877083..70879333,2	K562	blood:
5	chr1:70690194..70693110-chr1:70772753..70775116,2	K562	blood:
6	chr1:70667153..70674800-chr1:70681943..70693478,26	K562	blood:
7	chr1:70685268..70690578-chr1:70702989..70707451,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228988	TF binding region
SRSF11	TF binding region
ENSG00000066557	Chromatin interaction
ENSG00000116754	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10489927	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489928	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562802	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565362	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566666	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131235	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131248	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131251	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034756	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2210545	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274913	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297484	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297486	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2478801	0.83[AMR][1000 genomes]
rs34821575	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35262515	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753817	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767206	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767207	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767208	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767214	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920731	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4649913	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650031	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55727788	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58639674	0.86[ASN][1000 genomes]
rs58696538	0.85[EUR][1000 genomes]
rs58927829	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59234513	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60272091	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60441970	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs632517	0.83[AMR][1000 genomes]
rs668525	0.87[AMR][1000 genomes]
rs6702168	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716240	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74085992	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085996	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085999	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74088004	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088016	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088024	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088029	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74088032	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74088035	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088042	0.83[AMR][1000 genomes];0.92[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
rs56902977	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70687800-70691200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:70687800-70697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:70687800-70698600	Weak transcription	Gastric	stomach
4	chr1:70687800-70698800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:70687800-70699600	Weak transcription	Lung	lung
6	chr1:70687800-70699600	Weak transcription	Spleen	Spleen
7	chr1:70688000-70697200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:70688000-70697200	Weak transcription	Pancreas	Pancrea
9	chr1:70688000-70697800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:70688000-70699000	Weak transcription	Psoas Muscle	Psoas
11	chr1:70688000-70710400	Weak transcription	Aorta	Aorta
12	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
13	chr1:70688200-70690600	Weak transcription	Thymus	Thymus
14	chr1:70688200-70696200	Weak transcription	Colonic Mucosa	Colon
15	chr1:70688200-70708200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:70688400-70693000	Weak transcription	Fetal Stomach	stomach
17	chr1:70688400-70693800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:70688400-70719400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:70688600-70691400	Genic enhancers	Colon Smooth Muscle	Colon
20	chr1:70688600-70691800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:70688600-70719800	Strong transcription	Fetal Thymus	thymus
22	chr1:70688800-70690800	Genic enhancers	Duodenum Mucosa	Duodenum
23	chr1:70688800-70691000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:70688800-70691000	Genic enhancers	Liver	Liver
25	chr1:70688800-70691200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
26	chr1:70688800-70691600	Strong transcription	HSMM	muscle
27	chr1:70688800-70692400	Weak transcription	Right Atrium	heart
28	chr1:70688800-70692600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:70689000-70690600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:70689000-70690600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:70689000-70690600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:70689000-70690800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:70689000-70691200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:70689000-70692600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:70689000-70694800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:70689000-70717800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:70689000-70718200	Strong transcription	Placenta	Placenta
38	chr1:70689200-70690600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:70689200-70690600	Genic enhancers	A549	lung
40	chr1:70689200-70690800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:70689200-70691200	Genic enhancers	Fetal Heart	heart
42	chr1:70689200-70691200	Genic enhancers	Fetal Intestine Large	intestine
43	chr1:70689200-70692400	Weak transcription	Small Intestine	intestine
44	chr1:70689200-70697000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:70689200-70718600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:70689400-70690600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
47	chr1:70689400-70690600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:70689400-70690800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
49	chr1:70689400-70691000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr1:70689400-70691000	Genic enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links