Variant report

Variant	rs10238492
Chromosome Location	chr7:112434003-112434004
allele	A/G
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	CEBPB	chr7:112433976-112434123	HepG2	liver:	n/a	n/a
2	STAT3	chr7:112433919-112434914	MCF10A-Er-Src	breast:	n/a	chr7:112434697-112434708
3	STAT3	chr7:112433960-112434914	MCF10A-Er-Src	breast:	n/a	chr7:112434697-112434708
4	STAT3	chr7:112433945-112434873	MCF10A-Er-Src	breast:	n/a	chr7:112434697-112434708
5	STAT3	chr7:112433911-112435111	MCF10A-Er-Src	breast:	n/a	chr7:112434697-112434708
6	EP300	chr7:112433966-112434781	K562	blood:	n/a	n/a
7	JUND	chr7:112433934-112434180	K562	blood:	n/a	n/a
8	CEBPB	chr7:112433826-112434387	HCT-116	colon:	n/a	n/a
9	TEAD4	chr7:112433431-112434330	K562	blood:	n/a	chr7:112433664-112433673
10	CEBPB	chr7:112433918-112434218	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr7:112433935-112434099	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr7:112433661-112434400	HCT-116	colon:	n/a	n/a
13	CEBPB	chr7:112433914-112434189	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:112432334..112434564-chr7:112518600..112520396,2	K562	blood:
2	chr7:112431532..112434194-chr7:112463729..112466329,2	K562	blood:
3	chr7:112429019..112430745-chr7:112433310..112435464,2	MCF-7	breast:

Variant related genes	Relation type
TMEM168	TF binding region
ENSG00000146802	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10226382	0.91[ASN][1000 genomes]
rs10228483	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10233896	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10236439	0.82[YRI][hapmap]
rs10240478	0.82[YRI][hapmap]
rs10241725	0.82[YRI][hapmap]
rs10243834	0.87[AFR][1000 genomes]
rs10249952	1.00[JPT][hapmap]
rs10250630	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10253054	0.82[EUR][1000 genomes]
rs10256800	0.91[ASN][1000 genomes]
rs10257210	0.91[ASN][1000 genomes]
rs10259048	0.82[YRI][hapmap]
rs10261844	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10269437	0.82[YRI][hapmap]
rs10273589	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[TSI][hapmap]
rs10275208	0.84[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10277476	0.82[YRI][hapmap]
rs10280036	0.82[YRI][hapmap]
rs10280117	0.82[YRI][hapmap]
rs10280916	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1044262	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs11538991	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760733	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11762442	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11762737	0.91[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11768408	0.84[CEU][hapmap];0.82[CHD][hapmap]
rs11768787	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs11770088	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1227163	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs1227174	0.82[CHB][hapmap]
rs1227181	0.82[CHB][hapmap]
rs1227190	0.82[CHB][hapmap]
rs1238698	0.82[CHB][hapmap]
rs1530756	0.84[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs17160078	1.00[JPT][hapmap]
rs17405723	0.91[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1796492	0.82[CHB][hapmap]
rs1796493	0.82[CHB][hapmap]
rs1796516	0.82[CHB][hapmap]
rs1992988	0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2285541	0.82[CHB][hapmap];0.91[MEX][hapmap]
rs2396570	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs2457	0.82[CHB][hapmap]
rs2708296	0.82[CHB][hapmap]
rs28681358	0.91[ASN][1000 genomes]
rs3734956	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3957315	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56376790	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6466421	0.82[CHB][hapmap]
rs6944843	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7777973	0.82[CHB][hapmap]
rs7780098	0.85[ASN][1000 genomes]
rs7781871	0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs7803405	0.82[CHB][hapmap]
rs7806781	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7808616	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs9655816	0.87[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv2752144	chr7:112398372-112499924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv967494	chr7:112430613-112445931	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	nsv1031405	chr7:112431403-112476756	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10238492	CAV2	cis	parietal	SCAN
rs10238492	C7orf53	cis	parietal	SCAN
rs10238492	TES	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112430800-112440400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:112432400-112434800	Enhancers	K562	blood
3	chr7:112432800-112434400	Enhancers	NHEK	skin
4	chr7:112434000-112434200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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