Variant report

Variant	rs1494558
Chromosome Location	chr5:35861068-35861069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:35859166..35861325-chr5:35861673..35863431,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10044838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044883	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10058453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10063445	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10074095	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10074127	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10941267	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11567686	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11567717	0.83[YRI][hapmap]
rs11567737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353250	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1353252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389830	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1389831	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1389832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494555	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494556	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494557	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494562	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1862634	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3777090	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451227	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6451228	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451230	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451231	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6864736	0.82[YRI][hapmap]
rs6893142	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7701111	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7711202	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7711208	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711268	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7716064	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7720993	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292616	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9292617	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs969129	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881358	chr5:35850693-35861068	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv880610	chr5:35850693-35866265	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv880517	chr5:35850693-35870814	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv597813	chr5:35855264-35864590	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv881045	chr5:35856575-35861068	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv880591	chr5:35859863-35870588	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1494558	NIPBL	cis	parietal	SCAN
rs1494558	WDR70	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35852400-35862800	Enhancers	Hela-S3	cervix
2	chr5:35855400-35862400	Enhancers	HSMMtube	muscle
3	chr5:35857000-35861200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr5:35857000-35861400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:35857000-35861800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:35857400-35869200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr5:35857800-35866600	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr5:35858000-35862600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:35858000-35862600	Enhancers	NHDF-Ad	bronchial
10	chr5:35858200-35861600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:35858200-35863200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:35858200-35864800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:35858800-35862600	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr5:35858800-35864800	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:35858800-35865000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:35858800-35865400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:35858800-35866600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
18	chr5:35859000-35861200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:35859000-35862200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:35859000-35862600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:35859000-35864800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
22	chr5:35859000-35864800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
23	chr5:35859000-35865000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
24	chr5:35859200-35861400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr5:35859600-35861800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:35859600-35862200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
27	chr5:35859600-35862600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:35859600-35862600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:35859800-35861200	Enhancers	Osteobl	bone
30	chr5:35859800-35861600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:35859800-35863000	Weak transcription	Lung	lung
32	chr5:35860000-35861200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:35860000-35861600	Weak transcription	NHEK	skin
34	chr5:35860000-35862200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:35860000-35862800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:35860000-35869000	Weak transcription	HMEC	breast
37	chr5:35860000-35876600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:35860200-35862000	Weak transcription	NH-A	brain
39	chr5:35860200-35862000	Genic enhancers	NHLF	lung
40	chr5:35860200-35862200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:35860400-35861200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:35860400-35872800	Weak transcription	Spleen	Spleen
43	chr5:35860400-35883800	Weak transcription	Small Intestine	intestine
44	chr5:35860600-35861200	Enhancers	H9 Cell Line	embryonic stem cell
45	chr5:35860600-35861200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
46	chr5:35860600-35862000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr5:35860600-35862600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:35860600-35864800	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
49	chr5:35860800-35861200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr5:35860800-35861200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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