Variant report

Variant	rs12497539
Chromosome Location	chr3:156533937-156533938
allele	A/C
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:79824042..79825935-chr3:156533606..156535804,2	MCF-7	breast:
2	chr3:156426710..156429156-chr3:156532890..156534786,2	MCF-7	breast:
3	chr3:156531546..156534096-chr3:156793933..156795686,2	MCF-7	breast:
4	chr3:156533499..156536526-chr3:156891417..156894235,3	MCF-7	breast:
5	chr3:156400050..156402088-chr3:156531912..156534314,2	MCF-7	breast:
6	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
7	chr3:156398277..156399955-chr3:156533630..156535549,2	MCF-7	breast:
8	chr3:156497492..156500885-chr3:156532144..156534276,3	K562	blood:
9	chr3:156397478..156399872-chr3:156533478..156536173,2	MCF-7	breast:
10	chr3:156409514..156412147-chr3:156532498..156534140,2	K562	blood:
11	chr3:156532344..156534533-chr3:156884722..156886636,3	MCF-7	breast:
12	chr3:156533566..156537799-chr3:156875553..156879495,5	MCF-7	breast:
13	chr3:156256323..156258307-chr3:156531885..156534419,2	MCF-7	breast:
14	chr3:156533151..156536166-chr3:156876536..156878958,4	MCF-7	breast:
15	chr3:156389670..156395497-chr3:156530360..156537244,22	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163660	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000262413	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000243176	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10936037	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10936038	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11711674	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717133	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12492804	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072896	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13086516	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13097325	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1430410	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1430411	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1560415	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1560416	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1835372	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680305	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59717073	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6776157	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7641929	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9812169	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9820830	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9837271	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9842198	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9858861	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9874866	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12497539	LINC00886	cis	Adipose Subcutaneous	GTEx
rs12497539	LINC00886	cis	Muscle Skeletal	GTEx
rs12497539	LINC00886	cis	Esophagus Muscularis	GTEx
rs12497539	LINC00886	cis	Stomach	GTEx
rs12497539	LINC00886	cis	Nerve Tibial	GTEx
rs12497539	LINC00886	cis	Artery Aorta	GTEx
rs12497539	LINC00886	cis	Esophagus Mucosa	GTEx
rs12497539	LINC00886	cis	Thyroid	GTEx
rs12497539	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs12497539	LINC00886	cis	Artery Tibial	GTEx
rs12497539	LINC00886	cis	lung	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156531200-156534000	Weak transcription	Aorta	Aorta
2	chr3:156531200-156534000	Weak transcription	Gastric	stomach
3	chr3:156531200-156534200	Weak transcription	Stomach Mucosa	stomach
4	chr3:156531400-156534000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:156531400-156534600	Weak transcription	K562	blood
6	chr3:156531800-156534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:156533000-156534200	Bivalent Enhancer	Fetal Brain Male	brain
8	chr3:156533200-156534200	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr3:156533200-156535400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:156533200-156536200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:156533400-156534000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:156533400-156534000	Enhancers	Primary T cells from cord blood	blood
13	chr3:156533400-156534000	Enhancers	HepG2	liver
14	chr3:156533400-156534200	Flanking Active TSS	Liver	Liver
15	chr3:156533400-156534200	Flanking Active TSS	Fetal Intestine Small	intestine
16	chr3:156533400-156534400	Flanking Active TSS	NHDF-Ad	bronchial
17	chr3:156533400-156534600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:156533400-156534600	Flanking Active TSS	NH-A	brain
19	chr3:156533400-156535000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:156533400-156535200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr3:156533400-156535200	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr3:156533400-156535400	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr3:156533400-156535600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:156533600-156534000	Enhancers	Primary B cells from peripheral blood	blood
25	chr3:156533600-156534000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:156533600-156534000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:156533600-156534000	Enhancers	Fetal Heart	heart
28	chr3:156533600-156534000	Bivalent/Poised TSS	Fetal Stomach	stomach
29	chr3:156533600-156534000	Active TSS	Stomach Smooth Muscle	stomach
30	chr3:156533600-156534200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:156533600-156534200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr3:156533600-156534400	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:156533600-156534400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:156533600-156534400	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr3:156533600-156534400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr3:156533600-156534400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr3:156533600-156534600	Flanking Active TSS	Hela-S3	cervix
38	chr3:156533600-156534600	Flanking Active TSS	HUVEC	blood vessel
39	chr3:156533600-156535200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
40	chr3:156533600-156535200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:156533600-156535200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:156533600-156535200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:156533600-156535200	Active TSS	Brain Substantia Nigra	brain
44	chr3:156533600-156535200	Active TSS	Fetal Intestine Large	intestine
45	chr3:156533600-156535400	Active TSS	Colon Smooth Muscle	Colon
46	chr3:156533600-156535600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
47	chr3:156533600-156535600	Active TSS	Brain Anterior Caudate	brain
48	chr3:156533600-156535600	Active TSS	Brain Hippocampus Middle	brain
49	chr3:156533600-156535800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:156533600-156536000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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