Variant report

Variant	rs2657883
Chromosome Location	chr12:56851795-56851796
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	FOXA1	chr12:56851658-56851963	HepG2	liver:	n/a	n/a
2	FOXA1	chr12:56851670-56851952	HepG2	liver:	n/a	n/a
3	ARID3A	chr12:56851663-56851873	HepG2	liver:	n/a	chr12:56851676-56851692 chr12:56851677-56851693
4	FOXA2	chr12:56851683-56851904	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56846739..56849742-chr12:56851789..56854381,3	K562	blood:
2	chr12:56839650..56841550-chr12:56851154..56853411,2	MCF-7	breast:
3	chr12:56841744..56845737-chr12:56850366..56852697,3	K562	blood:

Variant related genes	Relation type
MIP	TF binding region
ENSG00000135517	Chromatin interaction
ENSG00000111602	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10876890	0.89[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs11171847	0.82[ASN][1000 genomes]
rs11171848	0.84[ASN][1000 genomes]
rs11171849	0.84[ASN][1000 genomes]
rs11171850	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs11171852	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs11171856	0.87[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs11610921	0.89[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs11833581	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs11833583	0.83[ASN][1000 genomes]
rs12299614	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs12313431	0.81[ASN][1000 genomes]
rs12316810	0.88[ASN][1000 genomes]
rs12815993	0.90[ASN][1000 genomes]
rs2279665	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2371455	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs2638304	0.81[ASN][1000 genomes]
rs2657882	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2939303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34520497	0.82[ASN][1000 genomes]
rs34644700	0.84[ASN][1000 genomes]
rs3782237	0.82[ASN][1000 genomes]
rs3809125	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs6581094	0.82[ASN][1000 genomes]
rs6581095	0.82[ASN][1000 genomes]
rs67027355	0.82[ASN][1000 genomes]
rs703829	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs7312888	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs774026	0.82[ASN][1000 genomes]
rs774027	0.81[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs774031	0.82[ASN][1000 genomes]
rs774032	0.82[ASN][1000 genomes]
rs774033	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs774034	0.85[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs774035	0.85[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs774036	0.80[CEU][hapmap];0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs774037	0.82[ASN][1000 genomes]
rs774039	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs774047	0.88[CEU][hapmap];0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs7977477	0.81[CEU][hapmap];0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs812279	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56843600-56852800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:56843800-56858000	Weak transcription	Brain Anterior Caudate	brain
3	chr12:56845000-56856400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:56848600-56856400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:56851200-56852600	Enhancers	Stomach Mucosa	stomach
6	chr12:56851600-56852200	Enhancers	HepG2	liver

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