Variant report

Variant	rs7819890
Chromosome Location	chr8:125186419-125186420
allele	C/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	chr8:125186280-125186430	HepG2	liver:	n/a	chr8:125186367-125186374
2	CTCF	chr8:125186354-125186423	Pancreas_OC	pancreas:	n/a	chr8:125186367-125186374
3	RAD21	chr8:125186228-125186439	K562	blood:	n/a	chr8:125186367-125186376
4	RAD21	chr8:125186022-125186594	MCF-7	breast:	n/a	chr8:125186367-125186376
5	RAD21	chr8:125186156-125186504	SK-N-SH_RA	brain:	n/a	chr8:125186367-125186376
6	CTCF	chr8:125186340-125186490	BE2_C	brain:	n/a	chr8:125186367-125186374
7	CTCF	chr8:125186280-125186430	GM12874	blood:	n/a	chr8:125186367-125186374
8	CTCF	chr8:125186298-125186422	MCF-7	breast:	n/a	chr8:125186367-125186374
9	CTCF	chr8:125186300-125186424	MCF-7	breast:	n/a	chr8:125186367-125186374
10	RAD21	chr8:125186063-125186579	HCT-116	colon:	n/a	chr8:125186367-125186376
11	RAD21	chr8:125186259-125186437	HepG2	liver:	n/a	chr8:125186367-125186376
12	RAD21	chr8:125186150-125186528	HCT-116	colon:	n/a	chr8:125186367-125186376
13	CTCF	chr8:125186280-125186430	MCF-7	breast:	n/a	chr8:125186367-125186374
14	RAD21	chr8:125186204-125186432	SK-N-SH_RA	brain:	n/a	chr8:125186367-125186376
15	CTCF	chr8:125186340-125186490	Caco-2	colon:	n/a	chr8:125186367-125186374
16	CTCF	chr8:125186320-125186470	SK-N-SH_RA	brain:	n/a	chr8:125186367-125186374
17	CTCF	chr8:125186280-125186430	HCT-116	colon:	n/a	chr8:125186367-125186374
18	CTCF	chr8:125186380-125186530	HCPEpiC	choroid plexus:	n/a	n/a
19	CTCF	chr8:125186343-125186462	GM13977	blood:	n/a	chr8:125186367-125186374
20	CTCF	chr8:125186282-125186449	HepG2	liver:	n/a	chr8:125186367-125186374
21	CTCF	chr8:125186280-125186430	GM12870	blood:	n/a	chr8:125186367-125186374
22	CTCF	chr8:125186296-125186461	K562	blood:	n/a	chr8:125186367-125186374
23	CTCF	chr8:125186066-125186646	MCF-7	breast:	n/a	chr8:125186367-125186374
24	CTCF	chr8:125186282-125186478	MCF-7	breast:	n/a	chr8:125186367-125186374
25	CTCF	chr8:125186306-125186464	MCF-7	breast:	n/a	chr8:125186367-125186374
26	CTCF	chr8:125186280-125186430	WERI-Rb-1	eye:	n/a	chr8:125186367-125186374
27	CTCF	chr8:125186225-125186512	K562	blood:	n/a	chr8:125186367-125186374
28	RAD21	chr8:125186113-125186598	MCF-7	breast:	n/a	chr8:125186367-125186376
29	CTCF	chr8:125186100-125186466	MCF-7	breast:	n/a	chr8:125186367-125186374
30	CTCF	chr8:125186360-125186510	GM12868	blood:	n/a	chr8:125186367-125186374
31	CTCF	chr8:125186238-125186513	T-47D	breast:	n/a	chr8:125186367-125186374
32	CTCF	chr8:125186320-125186422	NHEK	skin:	n/a	chr8:125186367-125186374
33	CTCF	chr8:125186280-125186430	GM12866	blood:	n/a	chr8:125186367-125186374
34	CTCF	chr8:125186280-125186430	K562	blood:	n/a	chr8:125186367-125186374
35	CTCF	chr8:125186335-125186429	HepG2	liver:	n/a	chr8:125186367-125186374
36	CTCF	chr8:125186280-125186430	GM12864	blood:	n/a	chr8:125186367-125186374

No.	Distal block	Cell Line	Cell type
1	chr8:125050107..125050678-chr8:125186177..125186793,3	MCF-7	breast:
2	chr8:125181319..125184229-chr8:125185870..125187642,2	K562	blood:
3	chr8:125181108..125183361-chr8:125183999..125186422,2	MCF-7	breast:
4	chr8:125186206..125188989-chr8:125282294..125285040,3	MCF-7	breast:

Variant related genes	Relation type
FER1L6-AS2	TF binding region
ENSG00000253868	Chromatin interaction
ENSG00000253227	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10091373	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10091745	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10091796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10097532	0.81[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap]
rs10102628	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs10103694	0.86[CHB][hapmap];0.83[GIH][hapmap]
rs10112410	0.81[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap]
rs10808532	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11775425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11776314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11777798	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11778782	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs11783004	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11783434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11784216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13252482	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13252741	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13278430	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs13282986	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985307	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28760335	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242354	0.86[CHB][hapmap]
rs4242355	0.86[CHB][hapmap]
rs4242357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4242358	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4242359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4321983	0.86[ASN][1000 genomes]
rs4338088	0.90[CHB][hapmap]
rs4363179	0.86[CHB][hapmap]
rs4366065	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380915	0.86[CHB][hapmap]
rs4388445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413755	0.86[CHB][hapmap];0.81[GIH][hapmap]
rs4413756	0.86[CHB][hapmap]
rs4415293	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs4431575	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap]
rs4434603	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs4455808	0.86[CHB][hapmap]
rs4567017	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4574828	0.86[CHB][hapmap]
rs4581038	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4613979	0.86[CHB][hapmap]
rs4870890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4870891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870892	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871463	0.81[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap]
rs4871467	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871468	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871469	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56353733	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6415484	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6470223	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs6982733	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6983946	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6984544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6984987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6985304	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6986145	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs6988185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6991000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6998116	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs6999726	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7000177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7005079	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7006141	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7008971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs7010103	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs7010277	0.81[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap]
rs7011521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7015546	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7016383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7017959	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7818609	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs7820397	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7833371	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs7834687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7837991	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7839182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7840464	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv612144	chr8:125057728-125206503	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1023183	chr8:125060532-125206445	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv948556	chr8:125067187-125204721	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv831452	chr8:125099708-125259926	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv891429	chr8:125163219-125246937	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7819890	FAM83A	cis	cerebellum	SCAN
rs7819890	POU5F1B	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125183000-125187200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr8:125184200-125193600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr8:125184400-125187200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr8:125184400-125187200	Weak transcription	Osteobl	bone
5	chr8:125184400-125187600	Weak transcription	NHEK	skin
6	chr8:125184400-125193600	Weak transcription	K562	blood
7	chr8:125184400-125195600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr8:125184600-125187200	Weak transcription	NHDF-Ad	bronchial
9	chr8:125185000-125187400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr8:125186000-125186800	Weak transcription	NHLF	lung
11	chr8:125186200-125189800	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links