Variant report

Variant	rs1028054
Chromosome Location	chr2:20294808-20294809
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20210274..20217508-chr2:20292118..20299922,13	MCF-7	breast:
2	chr2:20269147..20275842-chr2:20291951..20298996,12	MCF-7	breast:
3	chr2:20271401..20271935-chr2:20294339..20294859,2	MCF-7	breast:
4	chr2:20248110..20258329-chr2:20290320..20297278,22	MCF-7	breast:
5	chr2:20289699..20292359-chr2:20294103..20297412,3	MCF-7	breast:
6	chr2:20214925..20217152-chr2:20292879..20295056,3	MCF-7	breast:
7	chr2:20285176..20288161-chr2:20293130..20295136,2	MCF-7	breast:
8	chr2:20239345..20241750-chr2:20293079..20295990,2	K562	blood:
9	chr2:20247984..20253637-chr2:20287496..20297716,23	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000068697	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000223734	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];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10171384	1.00[CEU][hapmap];0.90[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];0.98[ASN][1000 genomes]
rs10195803	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10207632	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10208355	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs1028055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11096639	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11673841	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11677683	0.83[EUR][1000 genomes]
rs11677734	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs11679737	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs11682837	0.83[EUR][1000 genomes]
rs11685443	0.82[CEU][hapmap]
rs11685788	1.00[CEU][hapmap]
rs11689490	0.95[CEU][hapmap];0.80[CHB][hapmap];0.83[EUR][1000 genomes]
rs11690530	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11692546	0.87[CEU][hapmap]
rs11900576	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12998930	0.86[EUR][1000 genomes]
rs13005386	0.90[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs13391566	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs34694787	0.86[EUR][1000 genomes]
rs55971461	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62112180	0.83[EUR][1000 genomes]
rs6531203	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs6531204	0.91[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531205	0.91[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531206	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6531207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6708655	0.91[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6709349	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6719494	0.89[EUR][1000 genomes]
rs6749952	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7556745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561381	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs7572608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7582437	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7583420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7609013	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]
rs878983	0.85[CEU][hapmap]
rs907864	0.95[CEU][hapmap];0.86[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1028054	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20290400-20295400	Enhancers	HMEC	breast
2	chr2:20290800-20295200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:20291000-20300000	Weak transcription	Right Atrium	heart
4	chr2:20291600-20295200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr2:20291600-20295800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:20291600-20297800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:20291800-20295200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:20291800-20295200	Enhancers	NHEK	skin
9	chr2:20292000-20295400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:20292000-20300400	Weak transcription	HUVEC	blood vessel
11	chr2:20292200-20295400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:20293000-20295600	Enhancers	Liver	Liver
13	chr2:20293600-20295200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:20293600-20304200	Weak transcription	Stomach Mucosa	stomach
15	chr2:20294000-20297600	Weak transcription	Ovary	ovary
16	chr2:20294000-20297800	Weak transcription	Placenta	Placenta
17	chr2:20294000-20304400	Weak transcription	Pancreas	Pancrea
18	chr2:20294200-20297600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:20294200-20297600	Weak transcription	Esophagus	oesophagus
20	chr2:20294200-20297600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:20294200-20297600	Weak transcription	Hela-S3	cervix
22	chr2:20294200-20297600	Weak transcription	HSMM	muscle
23	chr2:20294200-20297600	Weak transcription	NHDF-Ad	bronchial
24	chr2:20294200-20297800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:20294400-20296200	Enhancers	HepG2	liver
26	chr2:20294400-20297400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:20294400-20297400	Weak transcription	HSMMtube	muscle
28	chr2:20294400-20297600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:20294400-20297600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:20294400-20297600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:20294400-20297600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:20294400-20297800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:20294400-20297800	Weak transcription	NH-A	brain
34	chr2:20294400-20300200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:20294600-20295000	Weak transcription	NHLF	lung
36	chr2:20294600-20297600	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:20294800-20297600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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