Variant report

Variant	rs62177860
Chromosome Location	chr2:160960571-160960572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:160942970..160945799-chr2:160958862..160960784,2	MCF-7	breast:
2	chr2:160954217..160956346-chr2:160959486..160961538,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10497209	0.83[AFR][1000 genomes]
rs10497210	0.83[AFR][1000 genomes]
rs10497213	1.00[ASN][1000 genomes]
rs10929965	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10929966	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12987602	1.00[ASN][1000 genomes]
rs1511218	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16844715	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17216980	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241792	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17241973	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17341301	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17831161	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17831191	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17831251	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17831329	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1870102	0.81[AFR][1000 genomes]
rs2124969	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2175416	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305819	0.84[ASN][1000 genomes]
rs34248629	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3749119	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4233681	1.00[ASN][1000 genomes]
rs4292050	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4363984	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4520993	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520994	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4637057	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664308	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4665147	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4665148	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56040145	0.83[AFR][1000 genomes]
rs56172865	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56293836	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56296079	0.83[AFR][1000 genomes]
rs56297666	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58354887	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59019419	0.85[AFR][1000 genomes]
rs59541669	0.85[AFR][1000 genomes]
rs60908067	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62175384	0.83[AFR][1000 genomes]
rs62175388	0.83[AFR][1000 genomes]
rs62175391	0.83[AFR][1000 genomes]
rs62175396	0.83[AFR][1000 genomes]
rs62175515	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62175517	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62175552	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177891	0.84[ASN][1000 genomes]
rs6707388	0.99[ASN][1000 genomes]
rs6707458	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6719686	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6728154	0.87[ASN][1000 genomes]
rs6731260	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6739867	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744567	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6759836	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6759924	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72621702	0.83[ASN][1000 genomes]
rs72979963	0.83[AFR][1000 genomes]
rs72982036	0.83[AFR][1000 genomes]
rs72982044	0.83[AFR][1000 genomes]
rs7563607	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7567781	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7586751	0.83[AFR][1000 genomes]
rs7593593	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs877200	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs925410	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs983916	0.83[AFR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62177860	LY75	cis	Esophagus Mucosa	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160950800-160967000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:160953200-160970800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:160954600-160970800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:160954600-160993000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:160954800-160963800	Weak transcription	Fetal Intestine Large	intestine
6	chr2:160954800-160966200	Weak transcription	Fetal Intestine Small	intestine
7	chr2:160955400-160965000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:160955800-160968800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:160956200-160965600	Strong transcription	HMEC	breast
10	chr2:160957000-160970200	Weak transcription	Pancreas	Pancrea
11	chr2:160957400-160981200	Weak transcription	Lung	lung
12	chr2:160958400-160965200	Strong transcription	NHEK	skin
13	chr2:160958600-160961200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:160958800-160960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:160959000-160960800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:160959200-160963800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:160959200-161004200	Weak transcription	Gastric	stomach
18	chr2:160959400-160962800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:160959400-160985200	Weak transcription	Esophagus	oesophagus
20	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
21	chr2:160959800-160960600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:160959800-160960800	Strong transcription	HSMM	muscle
23	chr2:160959800-160965800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:160960000-160966400	Weak transcription	HSMMtube	muscle
25	chr2:160960200-160960800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:160960400-160960800	Bivalent Enhancer	GM12878-XiMat	blood
27	chr2:160960400-160965600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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