Variant report

Variant	rs6591254
Chromosome Location	chr11:67346528-67346529
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	FOXA1	chr11:67346438-67346973	HepG2	liver:	n/a	chr11:67346848-67346860
2	EP300	chr11:67346492-67346926	HepG2	liver:	n/a	chr11:67346813-67346827
3	FOXA2	chr11:67346386-67347054	A549	lung:	n/a	chr11:67346848-67346860
4	HDAC2	chr11:67346502-67346873	HepG2	liver:	n/a	n/a
5	CEBPB	chr11:67346527-67346739	HepG2	liver:	n/a	n/a
6	CEBPB	chr11:67346441-67346840	HepG2	liver:	n/a	n/a
7	FOXA1	chr11:67346515-67346772	T-47D	breast:	n/a	n/a
8	CEBPB	chr11:67346474-67346792	K562	blood:	n/a	n/a
9	FOXA1	chr11:67346526-67346932	HepG2	liver:	n/a	chr11:67346848-67346860
10	FOXA1	chr11:67346517-67346984	HepG2	liver:	n/a	chr11:67346848-67346860
11	CEBPB	chr11:67346458-67346819	HepG2	liver:	n/a	n/a
12	SP1	chr11:67346465-67346859	HepG2	liver:	n/a	n/a
13	GATA3	chr11:67346481-67347516	MCF-7	breast:	n/a	chr11:67347334-67347344 chr11:67347335-67347344
14	NR2F2	chr11:67346500-67347040	MCF-7	breast:	n/a	n/a
15	CEBPB	chr11:67346443-67346809	K562	blood:	n/a	n/a
16	TEAD4	chr11:67346486-67346878	HepG2	liver:	n/a	n/a
17	FOXA2	chr11:67346217-67347201	HepG2	liver:	n/a	chr11:67346848-67346860
18	FOXA2	chr11:67346492-67346883	HepG2	liver:	n/a	chr11:67346848-67346860
19	TCF12	chr11:67346490-67346981	A549	lung:	n/a	n/a
20	RXRA	chr11:67346477-67346793	HepG2	liver:	n/a	chr11:67346769-67346785

No.	Distal block	Cell Line	Cell type
1	chr11:67344270..67346942-chr11:67379351..67381800,2	MCF-7	breast:
2	chr11:67307923..67310034-chr11:67344749..67347317,2	K562	blood:
3	chr11:67343427..67347334-chr11:67376017..67380328,4	K562	blood:
4	chr11:67344360..67352769-chr11:67395394..67400721,12	K562	blood:
5	chr11:67339734..67342343-chr11:67345681..67348171,3	MCF-7	breast:
6	chr11:67345086..67348074-chr11:67348502..67351412,2	K562	blood:

Variant related genes	Relation type
GSTP1	TF binding region
ENSG00000084207	Chromatin interaction
ENSG00000167799	Chromatin interaction
ENSG00000167792	Chromatin interaction
ENSG00000244152	Chromatin interaction
ENSG00000231793	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1079719	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10896181	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11603735	0.84[ASN][1000 genomes]
rs11605586	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17593068	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1871042	0.85[ASN][1000 genomes]
rs2370141	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370142	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370143	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36211089	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4930436	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55854833	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58046082	0.89[EUR][1000 genomes]
rs597297	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6591249	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591251	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591253	0.84[ASN][1000 genomes]
rs6591255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591256	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591258	0.85[ASN][1000 genomes]
rs7103713	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7106423	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7106675	0.91[EUR][1000 genomes]
rs7108426	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749174	0.84[ASN][1000 genomes]
rs762803	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7927657	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940813	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941395	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941648	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945035	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945927	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948478	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7948823	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7948911	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949394	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7949587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952081	0.92[EUR][1000 genomes]
rs947895	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
4	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
5	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
6	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
7	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
8	nsv1041988	chr11:67319916-67749246	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv897814	chr11:67339949-67460529	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv1050463	chr11:67343421-67717338	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
11	nsv1038189	chr11:67345320-67749246	Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
12	nsv1047236	chr11:67345320-67764068	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6591254	PTPRCAP	cis	Artery Tibial	GTEx
rs6591254	PTPRCAP	cis	Nerve Tibial	GTEx
rs6591254	PTPRCAP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67340600-67346800	Weak transcription	Pancreas	Pancrea
2	chr11:67340800-67346600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:67341400-67346600	Weak transcription	A549	lung
4	chr11:67342600-67347000	Weak transcription	Hela-S3	cervix
5	chr11:67343800-67346600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:67344400-67350600	Enhancers	Stomach Mucosa	stomach
7	chr11:67345000-67346800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:67345000-67346800	Weak transcription	Spleen	Spleen
9	chr11:67345000-67348400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:67345200-67346600	Weak transcription	K562	blood
11	chr11:67345200-67347200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:67345400-67346600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:67345400-67347400	Enhancers	Primary hematopoietic stem cells	blood
14	chr11:67345600-67346800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr11:67345600-67346800	Enhancers	HepG2	liver
16	chr11:67345600-67350200	Enhancers	Fetal Intestine Small	intestine
17	chr11:67346000-67347000	Weak transcription	Gastric	stomach
18	chr11:67346000-67347200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:67346000-67347200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr11:67346000-67348600	Enhancers	Fetal Intestine Large	intestine
21	chr11:67346000-67348800	Weak transcription	Placenta	Placenta
22	chr11:67346200-67346600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:67346200-67348000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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