Variant report

Variant	rs7609013
Chromosome Location	chr2:20292052-20292053
allele	A/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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20209743..20212701-chr2:20291274..20294214,2	MCF-7	breast:
2	chr2:20269147..20275842-chr2:20291951..20298996,12	MCF-7	breast:
3	chr2:20156943..20158580-chr2:20291492..20293656,2	MCF-7	breast:
4	chr2:20248110..20258329-chr2:20290320..20297278,22	MCF-7	breast:
5	chr2:20285871..20288708-chr2:20290874..20293778,2	MCF-7	breast:
6	chr2:20289699..20292359-chr2:20294103..20297412,3	MCF-7	breast:
7	chr2:20276734..20283198-chr2:20287354..20293786,7	MCF-7	breast:
8	chr2:20263940..20267235-chr2:20290862..20294236,4	MCF-7	breast:
9	chr2:20271820..20275999-chr2:20291191..20294413,6	MCF-7	breast:
10	chr2:20247984..20253637-chr2:20287496..20297716,23	MCF-7	breast:
11	chr2:20286111..20289844-chr2:20290692..20292976,3	MCF-7	breast:
12	chr2:20277155..20282170-chr2:20290246..20293600,5	MCF-7	breast:
13	chr2:20290689..20292864-chr2:20300791..20304475,3	K562	blood:
14	chr2:20230147..20231842-chr2:20291847..20293930,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223734	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000068697	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10169811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171384	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10195803	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10199614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207632	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208355	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs1028054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1028055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096639	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11673841	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11677683	0.83[EUR][1000 genomes]
rs11677734	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs11679737	0.86[CEU][hapmap]
rs11682837	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11685443	0.82[CEU][hapmap]
rs11685788	1.00[CEU][hapmap]
rs11689490	0.95[CEU][hapmap];0.80[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11690530	0.87[CEU][hapmap]
rs11692546	0.87[CEU][hapmap]
rs11900576	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12998930	0.87[EUR][1000 genomes]
rs13005386	0.90[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs13391566	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs34694787	0.85[EUR][1000 genomes]
rs55971461	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112180	0.84[EUR][1000 genomes]
rs6531203	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs6531204	0.91[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6531205	0.91[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6531206	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6708655	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6709349	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6719494	0.90[EUR][1000 genomes]
rs6749952	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561381	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7572608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582437	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7583420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878983	0.85[CEU][hapmap]
rs907864	0.95[CEU][hapmap];0.85[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7609013	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20288800-20293200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:20288800-20293200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:20289200-20293200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:20289800-20293400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:20290000-20293000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:20290000-20294400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:20290400-20294000	Enhancers	Placenta	Placenta
8	chr2:20290400-20295400	Enhancers	HMEC	breast
9	chr2:20290600-20292400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:20290600-20293600	Enhancers	Adipose Nuclei	Adipose
11	chr2:20290600-20294000	Enhancers	Fetal Heart	heart
12	chr2:20290600-20294400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:20290800-20292200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:20290800-20292200	Enhancers	Left Ventricle	heart
15	chr2:20290800-20292200	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:20290800-20294200	Enhancers	Esophagus	oesophagus
17	chr2:20290800-20294200	Enhancers	Fetal Stomach	stomach
18	chr2:20290800-20294400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:20290800-20294400	Enhancers	NH-A	brain
20	chr2:20290800-20295200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:20291000-20292200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:20291000-20292400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:20291000-20292400	Enhancers	Right Ventricle	heart
24	chr2:20291000-20293400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:20291000-20300000	Weak transcription	Right Atrium	heart
26	chr2:20291200-20292200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:20291200-20292400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:20291200-20293200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:20291200-20294400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:20291400-20293000	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:20291400-20293000	Enhancers	HepG2	liver
32	chr2:20291400-20294400	Enhancers	Psoas Muscle	Psoas
33	chr2:20291600-20292400	Enhancers	Colon Smooth Muscle	Colon
34	chr2:20291600-20292600	Enhancers	K562	blood
35	chr2:20291600-20293000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:20291600-20294600	Enhancers	NHLF	lung
37	chr2:20291600-20295200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:20291600-20295800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:20291600-20297800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:20291800-20292200	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr2:20291800-20292200	Enhancers	Osteobl	bone
42	chr2:20291800-20292600	Enhancers	A549	lung
43	chr2:20291800-20292800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:20291800-20293000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:20291800-20293200	Weak transcription	Ovary	ovary
46	chr2:20291800-20293200	Weak transcription	Hela-S3	cervix
47	chr2:20291800-20293400	Enhancers	Fetal Thymus	thymus
48	chr2:20291800-20293800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:20291800-20294000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:20291800-20294200	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links