Variant report

Variant	rs12692970
Chromosome Location	chr2:172594197-172594198
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	chr2:172581696..172584038-chr2:172591425..172594359,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077380	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10166005	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167419	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10174525	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10184866	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10194102	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200608	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10201419	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10204502	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10204622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10206062	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10207085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10497374	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10803863	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1113389	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11678984	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11757	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11886820	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11897196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11904009	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12053003	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12185567	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12692973	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12692974	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12692978	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13017585	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13018768	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022113	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13419987	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429113	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13429409	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474074	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554166	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1973706	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292815	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2357061	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2674484	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2678155	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs312916	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs312918	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs312919	0.91[AMR][1000 genomes]
rs312921	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs312924	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs312925	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34358700	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34542126	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35379278	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35391289	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35549875	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35645520	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35854280	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36057702	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770445	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770451	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770452	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795999	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667693	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667694	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4668407	0.81[EUR][1000 genomes]
rs4668412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668414	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6433311	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6433314	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66835971	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6705200	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6709156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6710698	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67204065	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6721680	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6722757	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724337	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6725388	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6738445	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6745143	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754817	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6757773	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6758704	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759575	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71013062	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7355523	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7355594	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7562356	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7572215	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7573003	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7586207	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7597387	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7604918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7608403	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs908670	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs908671	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs973889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv522519	chr2:172586567-172600310	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12692970	AC068039.4	cis	Thyroid	GTEx
rs12692970	AC068039.4	cis	Esophagus Mucosa	GTEx
rs12692970	AC068039.4	cis	Stomach	GTEx
rs12692970	AC068039.4	cis	Muscle Skeletal	GTEx
rs12692970	AC068039.4	cis	lung	GTEx
rs12692970	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs12692970	AC068039.4	cis	Esophagus Muscularis	GTEx
rs12692970	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs12692970	AC068039.4	cis	Heart Left Ventricle	GTEx
rs12692970	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs12692970	AC068039.4	cis	Whole Blood	GTEx
rs12692970	AC068039.4	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172546600-172602800	Weak transcription	Small Intestine	intestine
3	chr2:172559600-172605200	Weak transcription	Colonic Mucosa	Colon
4	chr2:172561400-172601800	Weak transcription	Fetal Heart	heart
5	chr2:172564200-172610000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:172569000-172618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:172569800-172611400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:172571400-172597800	Strong transcription	HSMM	muscle
9	chr2:172571800-172594200	Strong transcription	HUVEC	blood vessel
10	chr2:172572000-172595400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:172575400-172595600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:172579800-172595600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:172579800-172611200	Strong transcription	Adipose Nuclei	Adipose
14	chr2:172580000-172598000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr2:172580200-172595400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr2:172580200-172595400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:172580200-172595600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:172580200-172596000	Strong transcription	Primary hematopoietic stem cells	blood
19	chr2:172580200-172611200	Strong transcription	Placenta	Placenta
20	chr2:172580400-172595400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:172580400-172595600	Strong transcription	Primary T cells from cord blood	blood
22	chr2:172580400-172610600	Strong transcription	Fetal Thymus	thymus
23	chr2:172580400-172611400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:172580400-172611400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:172580600-172595400	Strong transcription	Primary B cells from cord blood	blood
26	chr2:172580800-172595600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:172581000-172595000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:172581000-172595400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:172581200-172601800	Weak transcription	Stomach Mucosa	stomach
30	chr2:172581400-172594200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:172581800-172608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:172581800-172611600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:172582200-172595600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:172582200-172595600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:172582400-172594200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:172582400-172595600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:172582600-172595400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:172583000-172595600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:172583600-172594600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:172584200-172605400	Strong transcription	Fetal Muscle Leg	muscle
41	chr2:172584800-172597200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:172586800-172600600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:172586800-172612000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:172587600-172600000	Weak transcription	Hela-S3	cervix
45	chr2:172587800-172594800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:172587800-172640800	Weak transcription	Psoas Muscle	Psoas
47	chr2:172588000-172595600	Strong transcription	Liver	Liver
48	chr2:172588400-172598000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:172588400-172601600	Weak transcription	Dnd41	blood
50	chr2:172588400-172601800	Weak transcription	H9 Cell Line	embryonic stem cell

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