Variant report

Variant	rs6661488
Chromosome Location	chr1:94057255-94057256
allele	A/C
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	MAX	chr1:94057163-94058270	ECC-1	luminal epithelium:	n/a	chr1:94057611-94057621
2	TCF12	chr1:94057191-94057797	HepG2	liver:	n/a	chr1:94057476-94057483 chr1:94057400-94057410
3	ATF2	chr1:94057189-94057888	GM12878	blood:	n/a	n/a
4	MYBL2	chr1:94056892-94058052	HepG2	liver:	n/a	n/a
5	FOXA1	chr1:94056892-94057867	HepG2	liver:	n/a	chr1:94057695-94057707
6	POLR2A	chr1:94057137-94058481	PFSK-1	brain:	n/a	n/a
7	SIN3AK20	chr1:94057241-94057721	PFSK-1	brain:	n/a	n/a
8	MBD4	chr1:94057120-94058544	HepG2	liver:	n/a	n/a
9	TCF12	chr1:94056879-94057428	A549	lung:	n/a	chr1:94057400-94057410
10	RUNX3	chr1:94057140-94057854	GM12878	blood:	n/a	n/a
11	EP300	chr1:94056874-94057981	HepG2	liver:	n/a	chr1:94057621-94057631 chr1:94057084-94057097
12	FOXA1	chr1:94056858-94057998	HepG2	liver:	n/a	chr1:94057695-94057707
13	NFIC	chr1:94057137-94057863	ECC-1	luminal epithelium:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
14	FOXA2	chr1:94057212-94057850	HepG2	liver:	n/a	chr1:94057695-94057707
15	CEBPB	chr1:94056909-94057760	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:94057236-94058879	HepG2	liver:	n/a	n/a
17	REST	chr1:94057220-94058152	HepG2	liver:	n/a	n/a
18	TBP	chr1:94057166-94058528	HepG2	liver:	n/a	n/a
19	FOSL2	chr1:94057218-94057943	HepG2	liver:	n/a	n/a
20	YY1	chr1:94057220-94058091	HepG2	liver:	n/a	n/a
21	MAX	chr1:94057250-94057734	K562	blood:	n/a	chr1:94057611-94057621
22	MYC	chr1:94056936-94057768	NB4	blood:	n/a	chr1:94057611-94057621
23	EBF1	chr1:94057035-94057642	GM12878	blood:	n/a	chr1:94057145-94057154 chr1:94057145-94057155
24	CHD2	chr1:94057025-94057477	GM12878	blood:	n/a	n/a
25	MTA3	chr1:94057232-94057834	GM12878	blood:	n/a	n/a
26	MXI1	chr1:94057018-94057935	SK-N-SH	brain:	n/a	chr1:94057400-94057409
27	HEY1	chr1:94056860-94058945	HepG2	liver:	n/a	n/a
28	FOXA1	chr1:94056868-94057858	HepG2	liver:	n/a	chr1:94057695-94057707
29	MYBL2	chr1:94056859-94058226	HepG2	liver:	n/a	n/a
30	RCOR1	chr1:94057193-94058084	HepG2	liver:	n/a	n/a
31	ELF1	chr1:94056907-94057923	HepG2	liver:	n/a	chr1:94057522-94057535
32	SPI1	chr1:94056885-94057464	HL-60	blood:	n/a	chr1:94057292-94057305
33	NFIC	chr1:94057102-94058256	ECC-1	luminal epithelium:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
34	ZC3H11A	chr1:94057253-94057353	K562	blood:	n/a	n/a
35	HNF4A	chr1:94057249-94057894	HepG2	liver:	n/a	n/a
36	RELA	chr1:94057059-94057829	GM19099	blood:	n/a	n/a
37	FOXM1	chr1:94057155-94057870	GM12878	blood:	n/a	n/a
38	EP300	chr1:94057060-94057803	HepG2	liver:	n/a	chr1:94057621-94057631 chr1:94057084-94057097
39	NFIC	chr1:94057191-94057924	GM12878	blood:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
40	MXI1	chr1:94057054-94058396	HepG2	liver:	n/a	chr1:94057400-94057409
41	POLR2A	chr1:94057002-94057957	PFSK-1	brain:	n/a	n/a
42	TAF1	chr1:94057060-94057720	PFSK-1	brain:	n/a	n/a
43	MAX	chr1:94056989-94057809	NB4	blood:	n/a	chr1:94057611-94057621
44	SP1	chr1:94056917-94057306	A549	lung:	n/a	chr1:94057062-94057076
45	POLR2A	chr1:94057252-94057804	GM12892	blood:	n/a	n/a
46	SP1	chr1:94056830-94057945	HepG2	liver:	n/a	chr1:94057062-94057076
47	FOXA2	chr1:94056838-94057512	A549	lung:	n/a	n/a
48	NFIC	chr1:94057013-94057850	SK-N-SH	brain:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
49	TEAD4	chr1:94057010-94057893	HepG2	liver:	n/a	n/a
50	MAX	chr1:94057088-94058422	HepG2	liver:	n/a	chr1:94057611-94057621

Variant related genes	Relation type
ENSG00000224093	TF binding region
BCAR3	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs17110124	0.98[ASN][1000 genomes]
rs2281474	0.91[ASN][1000 genomes]
rs2295330	0.90[CHB][hapmap]
rs236321	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs236322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236323	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236326	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236329	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236331	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs236332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236333	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236335	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs3767973	0.89[ASN][1000 genomes]
rs3767975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs3767976	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57012808	0.91[ASN][1000 genomes]
rs57466479	0.89[ASN][1000 genomes]
rs57914444	0.89[ASN][1000 genomes]
rs59777284	0.89[ASN][1000 genomes]
rs6671749	0.95[ASN][1000 genomes]
rs6674143	0.90[CHB][hapmap]
rs6692801	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516400	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518795	0.94[ASN][1000 genomes]
rs7519939	0.95[ASN][1000 genomes]
rs7524368	0.89[ASN][1000 genomes]
rs7551964	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6661488	EPHX4	cis	cerebellum	SCAN
rs6661488	BCAR3	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94041800-94059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:94043000-94058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:94046600-94058200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:94048200-94059200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:94048200-94059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:94049600-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:94050000-94059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:94050800-94057800	Weak transcription	Small Intestine	intestine
13	chr1:94050800-94059200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:94051400-94057600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:94052000-94057400	Weak transcription	Colonic Mucosa	Colon
16	chr1:94052400-94057600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:94053000-94058000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:94053000-94058000	Strong transcription	NHEK	skin
19	chr1:94053200-94058200	Strong transcription	NHDF-Ad	bronchial
20	chr1:94053400-94057600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:94053600-94058000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:94053600-94058000	Weak transcription	Right Atrium	heart
23	chr1:94053600-94063000	Genic enhancers	Muscle Satellite Cultured Cells	--
24	chr1:94054200-94057400	Strong transcription	Hela-S3	cervix
25	chr1:94054200-94058200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:94054200-94058400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:94054400-94061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:94054600-94057600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:94054600-94058400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:94054600-94062000	Weak transcription	Brain Substantia Nigra	brain
31	chr1:94054800-94057400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:94055000-94057400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:94055000-94057400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:94055000-94057400	Weak transcription	Gastric	stomach
35	chr1:94055000-94057600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:94055000-94058200	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:94055000-94059200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:94055200-94057400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:94055200-94058800	Enhancers	Primary hematopoietic stem cells	blood
40	chr1:94055400-94057800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:94055400-94057800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:94055600-94057400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:94055600-94057800	Weak transcription	Brain Anterior Caudate	brain
44	chr1:94055600-94058800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:94055800-94057400	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:94055800-94057400	Weak transcription	Lung	lung
47	chr1:94055800-94057400	Strong transcription	HSMM	muscle
48	chr1:94055800-94057800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:94055800-94058000	Weak transcription	HSMMtube	muscle
50	chr1:94055800-94058200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links