Variant report

Variant	rs59717073
Chromosome Location	chr3:156534245-156534246
allele	A/G
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	chr3:156533499..156536526-chr3:156891417..156894235,3	MCF-7	breast:
4	chr3:156400050..156402088-chr3:156531912..156534314,2	MCF-7	breast:
5	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
6	chr3:156398277..156399955-chr3:156533630..156535549,2	MCF-7	breast:
7	chr3:156497492..156500885-chr3:156532144..156534276,3	K562	blood:
8	chr3:156397478..156399872-chr3:156533478..156536173,2	MCF-7	breast:
9	chr3:156532344..156534533-chr3:156884722..156886636,3	MCF-7	breast:
10	chr11:62379524..62380293-chr3:156534229..156535226,2	Hela-S3	cervix:
11	chr12:120729906..120730464-chr3:156534039..156534816,2	Hela-S3	cervix:
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
ENSG00000222675	Chromatin interaction
ENSG00000262413	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000243176	Chromatin interaction
ENSG00000149489	Chromatin interaction
ENSG00000243926	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	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10936038	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711674	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717133	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12497539	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072896	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086516	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13097325	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560415	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560416	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1835372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680305	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776157	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641929	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9812169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9818684	0.81[AMR][1000 genomes]
rs9820830	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9837271	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842198	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858861	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

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
rs59717073	LINC00886	cis	Muscle Skeletal	GTEx
rs59717073	LINC00886	cis	Stomach	GTEx
rs59717073	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs59717073	LINC00886	cis	Nerve Tibial	GTEx
rs59717073	LINC00886	cis	Adipose Subcutaneous	GTEx
rs59717073	LINC00886	cis	lung	GTEx
rs59717073	LINC00886	cis	Artery Tibial	GTEx
rs59717073	LINC00886	cis	Artery Aorta	GTEx
rs59717073	LINC00886	cis	Thyroid	GTEx
rs59717073	LINC00886	cis	Esophagus Mucosa	GTEx
rs59717073	LINC00886	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156531400-156534600	Weak transcription	K562	blood
2	chr3:156531800-156534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:156533200-156535400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:156533200-156536200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:156533400-156534400	Flanking Active TSS	NHDF-Ad	bronchial
6	chr3:156533400-156534600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:156533400-156534600	Flanking Active TSS	NH-A	brain
8	chr3:156533400-156535000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:156533400-156535200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:156533400-156535200	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr3:156533400-156535400	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:156533400-156535600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr3:156533600-156534400	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:156533600-156534400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:156533600-156534400	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr3:156533600-156534400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr3:156533600-156534400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr3:156533600-156534600	Flanking Active TSS	Hela-S3	cervix
19	chr3:156533600-156534600	Flanking Active TSS	HUVEC	blood vessel
20	chr3:156533600-156535200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr3:156533600-156535200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:156533600-156535200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:156533600-156535200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:156533600-156535200	Active TSS	Brain Substantia Nigra	brain
25	chr3:156533600-156535200	Active TSS	Fetal Intestine Large	intestine
26	chr3:156533600-156535400	Active TSS	Colon Smooth Muscle	Colon
27	chr3:156533600-156535600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr3:156533600-156535600	Active TSS	Brain Anterior Caudate	brain
29	chr3:156533600-156535600	Active TSS	Brain Hippocampus Middle	brain
30	chr3:156533600-156535800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:156533600-156536000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:156533600-156536200	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:156533800-156534400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr3:156533800-156534400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:156533800-156534400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr3:156533800-156534400	Flanking Active TSS	Left Ventricle	heart
37	chr3:156533800-156534400	Flanking Active TSS	Pancreas	Pancrea
38	chr3:156533800-156534400	Flanking Active TSS	Right Ventricle	heart
39	chr3:156533800-156534600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr3:156533800-156534600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:156533800-156534800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr3:156533800-156535000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr3:156533800-156535000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr3:156533800-156535000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr3:156533800-156535000	Active TSS	HSMM	muscle
46	chr3:156533800-156535200	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr3:156533800-156535200	Bivalent/Poised TSS	Fetal Brain Female	brain
48	chr3:156533800-156535200	Active TSS	Fetal Kidney	kidney
49	chr3:156533800-156535200	Active TSS	Osteobl	bone
50	chr3:156533800-156535400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links