Variant report

Variant	rs804280
Chromosome Location	chr8:11612698-11612699
allele	G/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	CTCF	chr8:11612620-11612770	GM12878	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
2	CTCF	chr8:11612653-11612827	Hela-S3	cervix:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
3	CTCF	chr8:11612689-11612823	Fibrobl	skin:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
4	CTCF	chr8:11612695-11612796	ProgFib	skin:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
5	CTCF	chr8:11612560-11612710	HBMEC	blood vessel:	n/a	n/a
6	CTCF	chr8:11612478-11612909	A549	lung:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
7	CTCFL	chr8:11612638-11612788	K562	blood:	n/a	n/a
8	CTCF	chr8:11612620-11612770	MCF-7	breast:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
9	CTCFL	chr8:11612634-11612792	K562	blood:	n/a	n/a
10	CTCF	chr8:11612660-11612810	GM12875	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
11	RAD21	chr8:11612671-11612855	Hela-S3	cervix:	n/a	chr8:11612736-11612755
12	CTCF	chr8:11612653-11612842	MCF-7	breast:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
13	CTCF	chr8:11612660-11612810	K562	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
14	CTCF	chr8:11612640-11612790	HMEC	breast:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
15	RAD21	chr8:11612656-11612810	K562	blood:	n/a	chr8:11612736-11612755
16	CTCF	chr8:11612620-11612770	A549	lung:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
17	CTCF	chr8:11612600-11612750	GM12873	blood:	n/a	chr8:11612738-11612747
18	SMC3	chr8:11612615-11612865	K562	blood:	n/a	chr8:11612737-11612751
19	CTCF	chr8:11612567-11612820	A549	lung:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
20	RAD21	chr8:11612647-11612853	K562	blood:	n/a	chr8:11612736-11612755
21	CTCF	chr8:11612660-11612810	GM12865	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
22	RAD21	chr8:11612647-11612845	H1-hESC	embryonic stem cell:	n/a	chr8:11612736-11612755
23	CTCF	chr8:11612660-11612810	Hela-S3	cervix:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
24	CTCF	chr8:11612660-11612810	HBMEC	blood vessel:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
25	CTCF	chr8:11612690-11612794	MCF-7	breast:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
26	CTCF	chr8:11612600-11612750	AG10803	skin:	n/a	chr8:11612738-11612747
27	ELF1	chr8:11612424-11612876	K562	blood:	n/a	n/a
28	CTCF	chr8:11612672-11612804	A549	lung:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
29	CTCF	chr8:11612687-11612840	LNCaP	prostate:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
30	CTCF	chr8:11612620-11612770	GM12865	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
31	ELF1	chr8:11612534-11612906	MCF-7	breast:	n/a	n/a
32	CTCF	chr8:11612640-11612790	K562	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
33	CTCF	chr8:11612680-11612830	GM12865	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
34	CTCF	chr8:11612583-11612896	K562	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
35	CTCF	chr8:11612640-11612790	GM12874	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
36	CTCF	chr8:11612609-11612891	K562	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
37	CTCF	chr8:11612582-11612931	K562	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
38	ELF1	chr8:11612555-11612999	GM12878	blood:	n/a	n/a
39	CTCF	chr8:11612560-11612710	GM06990	blood:	n/a	n/a
40	CTCF	chr8:11612680-11612830	GM12871	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
41	CTCF	chr8:11612563-11612904	K562	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
42	CTCF	chr8:11612660-11612810	HMF	breast:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
43	CTCF	chr8:11612679-11612802	GM12878	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
44	CTCF	chr8:11612637-11612849	MCF-7	breast:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
45	CTCF	chr8:11612678-11612814	MCF-7	breast:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
46	CTCF	chr8:11612629-11612852	K562	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
47	CTCF	chr8:11612660-11612810	Caco-2	colon:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
48	CTCF	chr8:11612620-11612770	Caco-2	colon:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753
49	ELF1	chr8:11612529-11612864	K562	blood:	n/a	n/a
50	CTCF	chr8:11612665-11612840	GM12892	blood:	n/a	chr8:11612738-11612751 chr8:11612738-11612747 chr8:11612735-11612753

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11612285..11613206-chr8:11801217..11801735,2	MCF-7	breast:

Variant related genes	Relation type
GATA4	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1062219	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11250164	0.82[GIH][hapmap];0.94[MEX][hapmap]
rs11784693	0.82[GIH][hapmap];0.94[MEX][hapmap]
rs11784764	0.86[ASN][1000 genomes]
rs11785481	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13250578	1.00[JPT][hapmap]
rs13281294	1.00[JPT][hapmap]
rs2409814	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2645396	1.00[JPT][hapmap]
rs2645457	1.00[ASN][1000 genomes]
rs3735819	1.00[JPT][hapmap]
rs6991234	1.00[JPT][hapmap]
rs7006733	1.00[JPT][hapmap]
rs745379	1.00[ASN][1000 genomes]
rs804281	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804283	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs810738	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9644757	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS 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 target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv890359	chr8:11599570-11617240	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Myopia (pathological)	23049088	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs804280	CLDN23	cis	multi-tissue	Pritchard
rs804280	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs804280	DEFB134	cis	cerebellum	SCAN
rs804280	NEIL2	cis	Nerve Tibial	GTEx
rs804280	PRSS55	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11604400-11614400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:11604800-11616800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr8:11606000-11616200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:11606200-11617400	Strong transcription	HepG2	liver
5	chr8:11607000-11612800	Weak transcription	Right Ventricle	heart
6	chr8:11607000-11622800	Weak transcription	Stomach Mucosa	stomach
7	chr8:11608800-11619400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr8:11609200-11618600	Strong transcription	Ovary	ovary
9	chr8:11610200-11618400	Strong transcription	Liver	Liver
10	chr8:11610600-11621200	Strong transcription	Fetal Intestine Small	intestine
11	chr8:11610800-11615400	Enhancers	Fetal Heart	heart
12	chr8:11611000-11614400	Strong transcription	Gastric	stomach
13	chr8:11611200-11617000	Strong transcription	Placenta	Placenta
14	chr8:11611400-11618000	Strong transcription	Pancreas	Pancrea
15	chr8:11611600-11613800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr8:11611600-11614400	Weak transcription	Right Atrium	heart
17	chr8:11612400-11613000	Strong transcription	Fetal Intestine Large	intestine
18	chr8:11612600-11613200	Genic enhancers	Left Ventricle	heart
19	chr8:11612600-11614800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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