Variant report

Variant	rs6471514
Chromosome Location	chr8:96100272-96100273
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	NFIC	chr8:96099728-96100279	GM12878	blood:	n/a	n/a
2	MYC	chr8:96099847-96100327	MCF10A-Er-Src	breast:	n/a	n/a
3	MAX	chr8:96099615-96100560	NB4	blood:	n/a	n/a
4	TCF3	chr8:96100160-96100544	GM12878	blood:	n/a	chr8:96100300-96100310 chr8:96100298-96100312
5	MTA3	chr8:96099782-96100287	GM12878	blood:	n/a	n/a
6	POLR2A	chr8:96099845-96100582	HL-60	blood:	n/a	n/a
7	POLR2A	chr8:96099926-96100328	MCF10A-Er-Src	breast:	n/a	n/a
8	RUNX3	chr8:96099775-96100281	GM12878	blood:	n/a	n/a
9	MYC	chr8:96099887-96100307	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr8:96099959-96100668	MCF10A-Er-Src	breast:	n/a	n/a
11	SPI1	chr8:96099654-96100370	HL-60	blood:	n/a	chr8:96099933-96099942
12	POLR2A	chr8:96099728-96100538	HL-60	blood:	n/a	n/a
13	CTCF	chr8:96100240-96100390	GM12872	blood:	n/a	chr8:96100299-96100312
14	STAT3	chr8:96099908-96100378	MCF10A-Er-Src	breast:	n/a	chr8:96100091-96100103
15	FOXM1	chr8:96099809-96100289	GM12878	blood:	n/a	n/a
16	STAT3	chr8:96099893-96100375	MCF10A-Er-Src	breast:	n/a	chr8:96100091-96100103
17	FOS	chr8:96099592-96100327	MCF10A-Er-Src	breast:	n/a	chr8:96099935-96099944
18	STAT3	chr8:96099898-96100431	MCF10A-Er-Src	breast:	n/a	chr8:96100091-96100103
19	TCF12	chr8:96100184-96100448	GM12878	blood:	n/a	n/a
20	MYC	chr8:96099806-96100627	NB4	blood:	n/a	n/a
21	MAX	chr8:96100146-96100493	Hela-S3	cervix:	n/a	n/a
22	STAT3	chr8:96099829-96100314	MCF10A-Er-Src	breast:	n/a	chr8:96100091-96100103
23	EBF1	chr8:96099900-96100610	GM12878	blood:	n/a	n/a
24	STAT3	chr8:96099906-96100428	MCF10A-Er-Src	breast:	n/a	chr8:96100091-96100103
25	FOS	chr8:96099828-96100317	MCF10A-Er-Src	breast:	n/a	chr8:96099935-96099944
26	EBF1	chr8:96099905-96100536	GM12878	blood:	n/a	n/a
27	EBF1	chr8:96099974-96100355	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:95906412..95908805-chr8:96098165..96100293,2	MCF-7	breast:
2	chr8:96100209..96105308-chr8:96143573..96151809,12	K562	blood:
3	chr8:96095758..96103345-chr8:96144049..96152228,17	MCF-7	breast:
4	chr8:96096484..96101537-chr8:96142870..96147410,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254248	TF binding region
ENSG00000156170	Chromatin interaction
ENSG00000175305	Chromatin interaction
ENSG00000175895	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11778995	0.82[ASN][1000 genomes]
rs11785698	0.90[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1878736	0.84[AMR][1000 genomes]
rs1996500	1.00[CEU][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2119588	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165496	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165497	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599701	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2599702	1.00[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2599703	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2599704	0.85[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2599705	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2678839	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2678840	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28416970	0.83[ASN][1000 genomes]
rs2923814	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2945565	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945566	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824997	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4379417	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4641029	0.85[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6471509	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6471510	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6471513	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471515	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980872	0.82[ASN][1000 genomes]
rs6982086	0.90[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7002090	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7011768	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7011919	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966459	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9720421	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv891205	chr8:96062601-96115476	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
5	nsv891206	chr8:96092251-96115476	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6471514	STK3	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96080200-96101800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:96097600-96100800	Enhancers	Placenta	Placenta
3	chr8:96098000-96100800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr8:96098000-96100800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr8:96098200-96100800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr8:96098400-96101800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr8:96098400-96102400	Weak transcription	Stomach Mucosa	stomach
8	chr8:96098600-96101800	Weak transcription	Gastric	stomach
9	chr8:96098600-96101800	Weak transcription	HUVEC	blood vessel
10	chr8:96098600-96102000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr8:96098600-96102200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr8:96098600-96102200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr8:96098600-96102400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr8:96098600-96111600	Weak transcription	Pancreas	Pancrea
15	chr8:96098800-96102000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:96098800-96102200	Weak transcription	Thymus	Thymus
17	chr8:96098800-96102400	Weak transcription	Dnd41	blood
18	chr8:96098800-96103800	Weak transcription	HepG2	liver
19	chr8:96099200-96100600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr8:96099200-96100800	Enhancers	Primary B cells from peripheral blood	blood
21	chr8:96099600-96100400	Enhancers	Duodenum Mucosa	Duodenum
22	chr8:96099600-96100400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr8:96099600-96100400	Flanking Active TSS	NHEK	skin
24	chr8:96099600-96100600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr8:96099600-96101800	Enhancers	GM12878-XiMat	blood
26	chr8:96099800-96100400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr8:96099800-96100800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:96099800-96100800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr8:96099800-96101600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr8:96100000-96100400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr8:96100000-96100400	Enhancers	Adipose Nuclei	Adipose
32	chr8:96100000-96100600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr8:96100000-96100600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr8:96100000-96100600	Enhancers	Primary B cells from cord blood	blood
35	chr8:96100000-96100600	Enhancers	Spleen	Spleen
36	chr8:96100000-96100800	Enhancers	Esophagus	oesophagus
37	chr8:96100000-96100800	Enhancers	Fetal Thymus	thymus
38	chr8:96100000-96100800	Enhancers	Hela-S3	cervix
39	chr8:96100000-96100800	Enhancers	HMEC	breast
40	chr8:96100000-96101800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr8:96100000-96101800	Enhancers	K562	blood
42	chr8:96100000-96104200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr8:96100200-96100400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr8:96100200-96100400	Enhancers	Lung	lung
45	chr8:96100200-96100600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr8:96100200-96100600	Enhancers	Primary hematopoietic stem cells	blood
47	chr8:96100200-96100600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr8:96100200-96100600	Enhancers	Colonic Mucosa	Colon
49	chr8:96100200-96100600	Enhancers	Fetal Muscle Trunk	muscle
50	chr8:96100200-96100600	Enhancers	Rectal Mucosa Donor 31	rectum

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