Variant report

Variant	rs2679486
Chromosome Location	chr12:31773506-31773507
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	HNF4A	chr12:31773310-31773571	HepG2	liver:	n/a	n/a
2	MAFK	chr12:31773283-31773560	HepG2	liver:	n/a	n/a
3	HNF4G	chr12:31773194-31773667	HepG2	liver:	n/a	chr12:31773307-31773322 chr12:31773307-31773322
4	EP300	chr12:31773227-31773639	HepG2	liver:	n/a	chr12:31773563-31773573
5	RCOR1	chr12:31773376-31773545	HepG2	liver:	n/a	n/a
6	MAFK	chr12:31773263-31773540	HepG2	liver:	n/a	n/a
7	HNF4G	chr12:31773274-31773636	HepG2	liver:	n/a	chr12:31773307-31773322 chr12:31773307-31773322
8	TEAD4	chr12:31773150-31773648	HepG2	liver:	n/a	n/a
9	MAFF	chr12:31773263-31773564	HepG2	liver:	n/a	n/a
10	ARID3A	chr12:31773281-31773610	HepG2	liver:	n/a	n/a
11	SMC3	chr12:31773412-31773564	HepG2	liver:	n/a	n/a
12	CEBPB	chr12:31773329-31773559	HepG2	liver:	n/a	n/a
13	SP1	chr12:31773226-31773680	A549	lung:	n/a	n/a
14	EP300	chr12:31773394-31773509	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:31773297-31773623	K562	blood:	n/a	n/a
16	HDAC2	chr12:31773309-31773603	HepG2	liver:	n/a	n/a
17	HNF4A	chr12:31773308-31773555	HepG2	liver:	n/a	n/a
18	CEBPB	chr12:31773359-31773551	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31770731..31773142-chr12:31773203..31775587,2	K562	blood:

Variant related genes	Relation type
AK4P3	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10843975	0.84[JPT][hapmap]
rs11051486	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051497	0.85[ASN][1000 genomes]
rs12305966	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1677172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716207	0.90[ASN][1000 genomes]
rs2374170	0.84[JPT][hapmap]
rs2447707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2625881	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474909	0.85[ASN][1000 genomes]
rs476864	0.90[ASN][1000 genomes]
rs477758	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478620	0.93[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs509500	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529303	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538400	0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538430	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539102	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298559	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2474625	chr12:31773211-31774620	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31771200-31774600	Enhancers	Fetal Intestine Large	intestine
2	chr12:31771400-31775400	Enhancers	Fetal Intestine Small	intestine
3	chr12:31771600-31773600	Enhancers	HepG2	liver
4	chr12:31773000-31773600	Enhancers	A549	lung

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