Variant report

Variant	rs62175517
Chromosome Location	chr2:160911575-160911576
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	chr2:160908857..160913654-chr2:160916595..160920895,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153246	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10497209	0.83[AFR][1000 genomes]
rs10497210	0.83[AFR][1000 genomes]
rs10497213	0.83[ASN][1000 genomes]
rs10929965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12987602	0.83[ASN][1000 genomes]
rs1511218	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16844715	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17216980	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17241792	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17241973	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17341301	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17831161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17831191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17831251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17831329	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870102	0.81[AFR][1000 genomes]
rs2124969	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2175416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34248629	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749119	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4233681	0.83[ASN][1000 genomes]
rs4292050	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4363984	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4520993	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4520994	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4637057	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4664308	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4665147	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4665148	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56040145	0.83[AFR][1000 genomes]
rs56172865	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56293836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56296079	0.83[AFR][1000 genomes]
rs56297666	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58354887	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59019419	0.85[AFR][1000 genomes]
rs59541669	0.85[AFR][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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62175552	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62175559	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177860	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6705574	0.86[ASN][1000 genomes]
rs6707388	0.82[ASN][1000 genomes]
rs6707458	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6719686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731260	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6739867	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6744567	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6759836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6759924	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72621699	0.93[ASN][1000 genomes]
rs72621702	0.90[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7567781	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7586751	0.83[AFR][1000 genomes]
rs7593593	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs877200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925410	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs983916	0.83[AFR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62175517	LY75	cis	Esophagus Mucosa	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160881200-160912000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:160881200-160913400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:160884000-160911600	Weak transcription	Fetal Kidney	kidney
4	chr2:160895200-160911600	Weak transcription	HMEC	breast
5	chr2:160901400-160911800	Weak transcription	Adipose Nuclei	Adipose
6	chr2:160901600-160911600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:160903000-160913400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:160903800-160911600	Weak transcription	Esophagus	oesophagus
9	chr2:160908800-160917400	Weak transcription	NH-A	brain
10	chr2:160909000-160911600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:160909000-160918200	Weak transcription	Aorta	Aorta
12	chr2:160909200-160911600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:160909200-160911600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:160909200-160911600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:160909200-160911800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:160909200-160917000	Weak transcription	HSMMtube	muscle
17	chr2:160909400-160911600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:160909400-160911600	Weak transcription	Osteobl	bone
19	chr2:160909400-160911800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:160909400-160913400	Weak transcription	Fetal Intestine Small	intestine
21	chr2:160909400-160917200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:160909600-160911600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:160909600-160911800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:160909600-160911800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:160909800-160911800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:160909800-160913200	Weak transcription	Fetal Intestine Large	intestine
27	chr2:160909800-160917200	Weak transcription	NHEK	skin
28	chr2:160910200-160911600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:160910200-160911600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:160910400-160911600	Weak transcription	Ovary	ovary
31	chr2:160910400-160911800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:160910600-160911600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:160911400-160911600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr2:160911400-160911800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr2:160911400-160911800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:160911400-160911800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:160911400-160912000	Enhancers	Fetal Lung	lung
38	chr2:160911400-160912200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:160911400-160912200	Enhancers	Fetal Stomach	stomach
40	chr2:160911400-160912200	Enhancers	HUVEC	blood vessel
41	chr2:160911400-160912600	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:160911400-160912800	Enhancers	Rectal Smooth Muscle	rectum
43	chr2:160911400-160912800	Enhancers	NHDF-Ad	bronchial
44	chr2:160911400-160913000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:160911400-160913200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr2:160911400-160914600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:160911400-160914800	Enhancers	Colon Smooth Muscle	Colon

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