Variant report

Variant	rs55971461
Chromosome Location	chr2:20293548-20293549
allele	C/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:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20214859..20216804-chr2:20293145..20294071,9	MCF-7	breast:
2	chr2:20209743..20212701-chr2:20291274..20294214,2	MCF-7	breast:
3	chr2:20215034..20215891-chr2:20293118..20294150,7	MCF-7	breast:
4	chr2:20292117..20294039-chr2:20297489..20300259,2	MCF-7	breast:
5	chr2:20210274..20217508-chr2:20292118..20299922,13	MCF-7	breast:
6	chr2:20292423..20293956-chr2:20423516..20425711,2	MCF-7	breast:
7	chr2:20269147..20275842-chr2:20291951..20298996,12	MCF-7	breast:
8	chr2:20156943..20158580-chr2:20291492..20293656,2	MCF-7	breast:
9	chr2:20155249..20156315-chr2:20293113..20293893,6	MCF-7	breast:
10	chr2:20248110..20258329-chr2:20290320..20297278,22	MCF-7	breast:
11	chr2:20285871..20288708-chr2:20290874..20293778,2	MCF-7	breast:
12	chr2:20214925..20217152-chr2:20292879..20295056,3	MCF-7	breast:
13	chr2:20208609..20210141-chr2:20292705..20294742,2	MCF-7	breast:
14	chr2:20214992..20215965-chr2:20292746..20293998,6	K562	blood:
15	chr2:20263163..20266090-chr2:20292667..20294337,2	MCF-7	breast:
16	chr2:20276734..20283198-chr2:20287354..20293786,7	MCF-7	breast:
17	chr2:20155513..20156297-chr2:20293131..20294022,2	MCF-7	breast:
18	chr2:20285176..20288161-chr2:20293130..20295136,2	MCF-7	breast:
19	chr2:20263940..20267235-chr2:20290862..20294236,4	MCF-7	breast:
20	chr2:20271820..20275999-chr2:20291191..20294413,6	MCF-7	breast:
21	chr2:20155268..20156199-chr2:20293130..20294463,4	K562	blood:
22	chr2:20239345..20241750-chr2:20293079..20295990,2	K562	blood:
23	chr2:20247984..20253637-chr2:20287496..20297716,23	MCF-7	breast:
24	chr2:20277155..20282170-chr2:20290246..20293600,5	MCF-7	breast:
25	chr2:20287240..20289975-chr2:20292126..20294060,2	K562	blood:
26	chr2:20230147..20231842-chr2:20291847..20293930,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000068697	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000223734	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10169811	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171384	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10195803	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10199614	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207632	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208355	0.89[EUR][1000 genomes]
rs1028054	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1028055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096639	0.86[EUR][1000 genomes]
rs11673841	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11677683	0.83[EUR][1000 genomes]
rs11677734	0.81[EUR][1000 genomes]
rs11679737	0.80[EUR][1000 genomes]
rs11682837	0.83[EUR][1000 genomes]
rs11689490	0.83[EUR][1000 genomes]
rs11690530	0.80[EUR][1000 genomes]
rs11900576	0.90[EUR][1000 genomes]
rs12998930	0.86[EUR][1000 genomes]
rs13005386	0.86[EUR][1000 genomes]
rs13391566	0.89[EUR][1000 genomes]
rs34694787	0.86[EUR][1000 genomes]
rs62112180	0.83[EUR][1000 genomes]
rs6531203	0.93[EUR][1000 genomes]
rs6531204	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531205	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531206	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531207	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6708655	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6709349	0.86[EUR][1000 genomes]
rs6719494	0.89[EUR][1000 genomes]
rs6749952	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556745	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558628	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561381	0.94[EUR][1000 genomes]
rs7572608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582437	0.89[EUR][1000 genomes]
rs7583420	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609013	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907864	0.86[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55971461	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20290000-20294400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:20290400-20294000	Enhancers	Placenta	Placenta
3	chr2:20290400-20295400	Enhancers	HMEC	breast
4	chr2:20290600-20293600	Enhancers	Adipose Nuclei	Adipose
5	chr2:20290600-20294000	Enhancers	Fetal Heart	heart
6	chr2:20290600-20294400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:20290800-20294200	Enhancers	Esophagus	oesophagus
8	chr2:20290800-20294200	Enhancers	Fetal Stomach	stomach
9	chr2:20290800-20294400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:20290800-20294400	Enhancers	NH-A	brain
11	chr2:20290800-20295200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:20291000-20300000	Weak transcription	Right Atrium	heart
13	chr2:20291200-20294400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:20291400-20294400	Enhancers	Psoas Muscle	Psoas
15	chr2:20291600-20294600	Enhancers	NHLF	lung
16	chr2:20291600-20295200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:20291600-20295800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:20291600-20297800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:20291800-20293800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:20291800-20294000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:20291800-20294200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr2:20291800-20294400	Enhancers	Fetal Intestine Small	intestine
23	chr2:20291800-20294400	Weak transcription	Fetal Kidney	kidney
24	chr2:20291800-20295200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:20291800-20295200	Enhancers	NHEK	skin
26	chr2:20292000-20294200	Enhancers	HSMM	muscle
27	chr2:20292000-20294200	Enhancers	NHDF-Ad	bronchial
28	chr2:20292000-20294400	Enhancers	Fetal Muscle Trunk	muscle
29	chr2:20292000-20294800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:20292000-20295400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:20292000-20300400	Weak transcription	HUVEC	blood vessel
32	chr2:20292200-20294600	Enhancers	Fetal Muscle Leg	muscle
33	chr2:20292200-20295400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:20292400-20293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:20292400-20293800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:20292800-20293600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr2:20292800-20294000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:20293000-20294000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:20293000-20294000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:20293000-20294000	Enhancers	Pancreas	Pancrea
41	chr2:20293000-20294200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:20293000-20294200	Enhancers	Fetal Intestine Large	intestine
43	chr2:20293000-20294200	Enhancers	A549	lung
44	chr2:20293000-20294400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:20293000-20294400	Flanking Active TSS	HepG2	liver
46	chr2:20293000-20295600	Enhancers	Liver	Liver
47	chr2:20293200-20293600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:20293200-20293600	Enhancers	Stomach Mucosa	stomach
49	chr2:20293200-20293800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:20293200-20293800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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