Variant report

Variant	rs13241786
Chromosome Location	chr7:100486656-100486657
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100302488..100305264-chr7:100484983..100487146,3	K562	blood:
2	chr7:100486439..100489230-chr7:100726552..100729974,6	MCF-7	breast:
3	chr7:100418397..100419909-chr7:100486584..100488563,2	MCF-7	breast:
4	chr7:100303615..100305529-chr7:100486314..100489038,2	K562	blood:
5	chr7:100485568..100489865-chr7:100727204..100729829,6	MCF-7	breast:
6	chr7:100486144..100489424-chr7:100805467..100808505,5	MCF-7	breast:
7	chr7:100024866..100028113-chr7:100485356..100489963,5	MCF-7	breast:
8	chr7:100269556..100272634-chr7:100485447..100488529,3	K562	blood:
9	chr7:100269920..100272546-chr7:100486381..100488020,2	MCF-7	breast:
10	chr3:125093829..125095736-chr7:100486331..100489025,2	MCF-7	breast:
11	chr7:100485751..100487913-chr7:100611034..100613104,2	K562	blood:
12	chr7:100486155..100488924-chr7:100732323..100735470,4	MCF-7	breast:
13	chr7:100486624..100489424-chr7:100545614..100548228,2	MCF-7	breast:
14	chr6:42749094..42751752-chr7:100485925..100488500,3	MCF-7	breast:
15	chr7:100447367..100452420-chr7:100484839..100489079,9	MCF-7	breast:
16	chr7:100223306..100225539-chr7:100484655..100487462,2	K562	blood:
17	chr7:100486587..100489014-chr7:100735698..100737931,3	MCF-7	breast:
18	chr7:100485984..100488072-chr7:100806477..100808899,2	K562	blood:
19	chr7:100448922..100451627-chr7:100483976..100487908,4	K562	blood:
20	chr7:100299982..100306646-chr7:100485585..100490991,8	MCF-7	breast:
21	chr7:100201842..100204261-chr7:100485824..100488204,2	MCF-7	breast:
22	chr7:100208465..100211590-chr7:100485559..100488810,4	MCF-7	breast:
23	chr7:100486477..100489401-chr7:100859928..100862607,2	MCF-7	breast:
24	chr7:100484134..100489082-chr7:100804986..100809404,8	MCF-7	breast:
25	chr7:100486083..100488238-chr7:100659648..100662388,2	MCF-7	breast:
26	chr7:100423550..100425060-chr7:100485976..100488045,2	K562	blood:
27	chr7:100423424..100426106-chr7:100484562..100490364,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196411	Chromatin interaction
ENSG00000128564	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000263672	Chromatin interaction
ENSG00000260336	Chromatin interaction
ENSG00000227053	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000225946	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000169894	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000172354	Chromatin interaction
ENSG00000163848	Chromatin interaction
ENSG00000106397	Chromatin interaction
ENSG00000112624	Chromatin interaction
ENSG00000228273	Chromatin interaction
ENSG00000236305	Chromatin interaction
ENSG00000169871	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000106400	Chromatin interaction
ENSG00000205277	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1054391	0.89[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11973000	0.84[EUR][1000 genomes]
rs11978697	0.86[EUR][1000 genomes]
rs12666785	0.85[CEU][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12669120	0.85[CEU][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12672665	0.89[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12705094	0.85[CEU][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs13226043	0.90[ASN][1000 genomes]
rs13232524	0.82[EUR][1000 genomes]
rs15624	0.89[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1799806	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2405973	0.82[EUR][1000 genomes]
rs2405974	0.81[EUR][1000 genomes]
rs2405975	0.83[EUR][1000 genomes]
rs2571598	0.87[EUR][1000 genomes]
rs2720392	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs28852509	0.93[EUR][1000 genomes]
rs2894713	0.85[EUR][1000 genomes]
rs3087504	0.85[CEU][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs314330	0.86[EUR][1000 genomes]
rs314369	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs314371	0.88[ASN][1000 genomes]
rs314372	0.86[ASN][1000 genomes]
rs314374	0.85[CEU][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs314375	0.89[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs314376	0.85[CEU][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs314377	0.89[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs314378	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34005963	0.84[EUR][1000 genomes]
rs3757869	0.85[EUR][1000 genomes]
rs3757870	0.85[EUR][1000 genomes]
rs3757871	0.84[EUR][1000 genomes]
rs3847063	0.85[CEU][hapmap]
rs3847064	0.85[EUR][1000 genomes]
rs3847068	0.84[EUR][1000 genomes]
rs3931823	0.85[EUR][1000 genomes]
rs4727469	0.85[CEU][hapmap]
rs4729615	0.89[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4729616	0.85[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs4729617	0.89[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4729618	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs4729619	0.85[EUR][1000 genomes]
rs4729620	0.85[CEU][hapmap]
rs6465776	0.89[CEU][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6942607	0.85[CEU][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6954151	0.85[CEU][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6976053	0.82[CEU][hapmap]
rs7783457	0.85[CEU][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7783543	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7794532	0.82[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs7798613	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7801015	0.90[ASN][1000 genomes]
rs7803865	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
12	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
13	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
14	nsv888802	chr7:100484917-100495530	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
15	nsv607967	chr7:100486016-100487748	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv607968	chr7:100486035-100492896	Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	39 gene(s)	inside rSNPs	diseases
17	nsv888803	chr7:100486656-100497131	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13241786	ZNF3	cis	parietal	SCAN
rs13241786	PLOD3	cis	cerebellum	SCAN
rs13241786	SHFM1	cis	cerebellum	SCAN
rs13241786	ENSG00000176125	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100482800-100487200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:100483800-100486800	Genic enhancers	Spleen	Spleen
3	chr7:100484600-100486800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:100484600-100486800	Enhancers	Fetal Heart	heart
5	chr7:100484800-100486800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
6	chr7:100484800-100487000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr7:100484800-100487000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:100484800-100487400	Enhancers	Stomach Mucosa	stomach
9	chr7:100484800-100488800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr7:100485000-100486800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr7:100485000-100487000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
12	chr7:100485000-100487000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:100485400-100486800	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
14	chr7:100485400-100487000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:100485600-100486800	Transcr. at gene 5' and 3'	HSMM	muscle
16	chr7:100485600-100487000	Transcr. at gene 5' and 3'	A549	lung
17	chr7:100485600-100487200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:100485800-100487200	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr7:100486000-100486800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:100486000-100486800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr7:100486000-100486800	Weak transcription	Aorta	Aorta
22	chr7:100486000-100487000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr7:100486000-100487000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
24	chr7:100486000-100488400	Active TSS	Psoas Muscle	Psoas
25	chr7:100486200-100486800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:100486200-100486800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:100486200-100486800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:100486200-100486800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:100486200-100487000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:100486200-100487000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
31	chr7:100486200-100487200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr7:100486200-100487400	Enhancers	Fetal Brain Male	brain
33	chr7:100486200-100489000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:100486400-100486800	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:100486400-100486800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:100486400-100486800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:100486400-100486800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:100486400-100486800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:100486400-100486800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr7:100486400-100486800	Flanking Active TSS	Esophagus	oesophagus
41	chr7:100486400-100486800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
42	chr7:100486400-100486800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
43	chr7:100486400-100486800	Flanking Active TSS	NHDF-Ad	bronchial
44	chr7:100486400-100486800	Flanking Active TSS	Osteobl	bone
45	chr7:100486400-100487000	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr7:100486400-100487000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr7:100486400-100487000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:100486400-100487000	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr7:100486400-100487000	Flanking Active TSS	NH-A	brain
50	chr7:100486400-100487200	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived

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