Variant report

Variant	rs62109431
Chromosome Location	chr2:20230156-20230157
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20230147..20231842-chr2:20291847..20293930,2	MCF-7	breast:
2	chr2:20228835..20232781-chr2:20233072..20236989,5	MCF-7	breast:
3	chr2:20225886..20230691-chr2:20231442..20234777,5	MCF-7	breast:
4	chr2:20228828..20231384-chr2:20242994..20245611,2	K562	blood:

Variant related genes	Relation type
ENSG00000068697	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016316	0.93[EUR][1000 genomes]
rs11674251	0.93[ASN][1000 genomes]
rs11689320	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11689431	0.88[ASN][1000 genomes]
rs11694170	0.93[EUR][1000 genomes]
rs11695154	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1191805	0.85[EUR][1000 genomes]
rs1191817	0.85[EUR][1000 genomes]
rs12988954	0.94[ASN][1000 genomes]
rs1473887	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1473890	0.93[EUR][1000 genomes]
rs1513830	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513831	0.93[EUR][1000 genomes]
rs16987338	0.92[EUR][1000 genomes]
rs34539547	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36071721	0.92[EUR][1000 genomes]
rs3731673	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769759	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769760	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769762	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62109427	0.86[ASN][1000 genomes]
rs6706375	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6720508	0.93[EUR][1000 genomes]
rs7558777	0.91[EUR][1000 genomes]
rs7558988	0.89[EUR][1000 genomes]
rs7570360	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7587612	0.92[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62109431	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20213400-20232200	Weak transcription	Right Ventricle	heart
2	chr2:20221400-20233200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:20221400-20249800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:20222400-20231200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:20222800-20233200	Weak transcription	Right Atrium	heart
6	chr2:20223000-20233000	Weak transcription	NHEK	skin
7	chr2:20223800-20232200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:20225200-20231000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:20225400-20231200	Weak transcription	HMEC	breast
10	chr2:20225400-20240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:20225800-20230600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:20225800-20232600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:20226400-20231000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:20226600-20236200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:20226800-20232600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:20226800-20236200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:20227000-20230400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr2:20227000-20230800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:20227000-20231800	Strong transcription	Brain Hippocampus Middle	brain
20	chr2:20227000-20234200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:20227000-20236200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:20227000-20239800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:20227000-20240200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:20227000-20240200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:20227000-20240600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:20227000-20240800	Strong transcription	Placenta	Placenta
27	chr2:20227000-20241000	Strong transcription	Liver	Liver
28	chr2:20227000-20242000	Strong transcription	Primary T cells from cord blood	blood
29	chr2:20227000-20242400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:20227200-20230400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:20227200-20233000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:20227200-20235800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:20227200-20236000	Strong transcription	Primary B cells from cord blood	blood
34	chr2:20227200-20240200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:20227200-20240800	Strong transcription	Fetal Lung	lung
36	chr2:20227200-20241000	Strong transcription	Fetal Thymus	thymus
37	chr2:20227200-20242200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:20227400-20231600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:20227400-20235000	Strong transcription	Fetal Kidney	kidney
40	chr2:20227400-20240800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:20227400-20240800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:20227400-20240800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:20227600-20236000	Weak transcription	Stomach Mucosa	stomach
44	chr2:20227600-20240400	Strong transcription	Adipose Nuclei	Adipose
45	chr2:20227600-20241000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:20227800-20230400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr2:20227800-20233000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:20227800-20236200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr2:20227800-20241200	Strong transcription	Fetal Intestine Large	intestine
50	chr2:20227800-20242200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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