Variant report

Variant	rs6959836
Chromosome Location	chr7:5099367-5099368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5097305..5100194-chr7:5103696..5105358,2	MCF-7	breast:
2	chr7:5094315..5096516-chr7:5099109..5101709,3	K562	blood:
3	chr7:5098780..5102439-chr7:5104196..5107618,3	K562	blood:
4	chr7:5098780..5101598-chr7:5103021..5105696,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10227289	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10231607	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10234867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10244918	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10247778	0.89[ASN][1000 genomes]
rs10258371	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10266832	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10268122	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10270777	0.82[EUR][1000 genomes]
rs10274596	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10276341	0.89[ASN][1000 genomes]
rs28378446	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28584451	0.83[EUR][1000 genomes]
rs28645895	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28770605	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3924251	0.89[ASN][1000 genomes]
rs4475394	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4548076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55787911	0.89[ASN][1000 genomes]
rs57875076	0.89[ASN][1000 genomes]
rs59887595	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60629388	0.89[ASN][1000 genomes]
rs6463203	1.00[CHD][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs6463205	0.88[CEU][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs6463207	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6463230	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6463231	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6463235	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67717765	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6949280	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs6961168	0.89[ASN][1000 genomes]
rs6961190	0.89[ASN][1000 genomes]
rs6961334	0.89[ASN][1000 genomes]
rs6971146	0.89[ASN][1000 genomes]
rs6978131	0.89[ASN][1000 genomes]
rs6979525	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73046002	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73051675	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73051676	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73051679	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73051685	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73673288	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7777964	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7797055	0.89[ASN][1000 genomes]
rs7797127	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7798073	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7798542	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7798891	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7799248	0.89[ASN][1000 genomes]
rs7800011	0.89[ASN][1000 genomes]
rs7802590	0.82[EUR][1000 genomes]
rs7803740	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
8	nsv1019120	chr7:4929653-5138409	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv917078	chr7:4962123-5151633	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1029430	chr7:5053887-5223583	Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv1034446	chr7:5066181-5108770	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1025644	chr7:5066181-5114089	Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1032880	chr7:5066181-5205932	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv1030384	chr7:5066181-5210555	Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6959836	FSCN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5086400-5101400	Weak transcription	Stomach Mucosa	stomach
2	chr7:5086800-5109200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:5088200-5107400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:5088200-5111400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:5088400-5108800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr7:5088400-5109600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr7:5088600-5108600	ZNF genes & repeats	Dnd41	blood
8	chr7:5088800-5100200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:5088800-5107200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:5089200-5108800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr7:5089200-5110400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr7:5089400-5105200	ZNF genes & repeats	GM12878-XiMat	blood
13	chr7:5089400-5107600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr7:5089400-5110200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:5089600-5108400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr7:5089600-5110400	ZNF genes & repeats	Liver	Liver
17	chr7:5090600-5100000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:5091000-5105200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
19	chr7:5091000-5110200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:5091400-5108400	ZNF genes & repeats	Fetal Lung	lung
21	chr7:5091400-5108600	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr7:5092400-5100600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:5092800-5100200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:5092800-5100800	Strong transcription	Fetal Thymus	thymus
25	chr7:5092800-5105400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:5093200-5099600	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:5093400-5101400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:5093400-5105400	ZNF genes & repeats	Fetal Muscle Leg	muscle
29	chr7:5093600-5099400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr7:5093600-5099600	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr7:5093600-5100200	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:5093800-5100200	Strong transcription	Placenta	Placenta
33	chr7:5094000-5099800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:5094200-5099400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:5094600-5106800	Strong transcription	HepG2	liver
36	chr7:5094800-5100200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr7:5094800-5100200	Strong transcription	HSMM	muscle
38	chr7:5094800-5100400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:5095000-5099400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr7:5095200-5108600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr7:5095200-5111600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
42	chr7:5095400-5100200	Strong transcription	NH-A	brain
43	chr7:5095400-5110200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr7:5096000-5100200	Strong transcription	Colonic Mucosa	Colon
45	chr7:5096000-5108600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:5096000-5108600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:5096200-5099600	Strong transcription	Rectal Smooth Muscle	rectum
48	chr7:5096200-5099600	Strong transcription	HSMMtube	muscle
49	chr7:5096200-5100000	Strong transcription	NHDF-Ad	bronchial
50	chr7:5096400-5099400	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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