Variant report

Variant	rs12987513
Chromosome Location	chr2:233622066-233622067
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233619490..233621276-chr2:233621324..233622956,2	MCF-7	breast:
2	chr2:233620394..233622879-chr2:233628718..233631332,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204120	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1022330	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1044480	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933409	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933411	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10933412	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11555646	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676216	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11679079	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687128	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690474	0.87[EUR][1000 genomes]
rs11692545	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12472839	0.96[EUR][1000 genomes]
rs12474040	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478564	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694917	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12990821	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12991088	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997185	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13003675	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13003738	0.81[ASN][1000 genomes]
rs13004406	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13007783	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13008942	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011298	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013142	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021246	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024793	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13035829	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13424351	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1446308	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446310	0.91[ASN][1000 genomes]
rs1446311	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1801251	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867778	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1947105	0.82[EUR][1000 genomes]
rs2012221	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2044449	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2100053	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2305137	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2305141	0.91[ASN][1000 genomes]
rs2592102	0.82[EUR][1000 genomes]
rs2592105	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592113	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2674839	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2675971	0.82[EUR][1000 genomes]
rs2675973	0.82[EUR][1000 genomes]
rs2675974	0.82[EUR][1000 genomes]
rs283466	0.91[ASN][1000 genomes]
rs283468	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs283469	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs283471	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs283474	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283475	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283476	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs283477	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs283478	0.82[ASN][1000 genomes]
rs283479	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283480	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283481	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283484	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283485	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283486	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33980184	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880628	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35085837	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35212961	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35285732	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35362030	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35395584	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35621474	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36007169	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816334	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3817311	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452130	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4458205	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4517962	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4973053	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4973054	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4973056	0.80[EUR][1000 genomes]
rs4973559	0.81[ASN][1000 genomes]
rs4973560	0.88[ASN][1000 genomes]
rs4973561	0.91[ASN][1000 genomes]
rs56777991	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437074	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66549961	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67013068	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714245	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717841	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719061	0.89[ASN][1000 genomes]
rs6724117	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732136	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733151	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738386	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739638	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745879	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746294	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6747645	0.97[EUR][1000 genomes]
rs6748027	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761324	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71421663	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737028	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558609	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7562712	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7573208	0.89[ASN][1000 genomes]
rs7578299	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587309	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7589201	0.82[EUR][1000 genomes]
rs7591176	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7592717	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606090	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778166	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs895430	0.82[EUR][1000 genomes]
rs9653383	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9679089	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs983430	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs991873	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12987513	C2orf82	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	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:233571200-233627400	Weak transcription	Gastric	stomach
3	chr2:233585200-233655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:233585800-233626000	Weak transcription	Fetal Heart	heart
5	chr2:233587000-233630600	Weak transcription	Psoas Muscle	Psoas
6	chr2:233589600-233627000	Weak transcription	Pancreas	Pancrea
7	chr2:233597200-233627000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:233602400-233633200	Weak transcription	Aorta	Aorta
9	chr2:233606200-233638400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:233606800-233633200	Weak transcription	Stomach Mucosa	stomach
11	chr2:233606800-233636800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:233609200-233630800	Strong transcription	HepG2	liver
13	chr2:233611000-233628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:233611400-233623800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:233611600-233623600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:233611600-233645600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:233611800-233622600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:233611800-233623000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:233612000-233622400	Strong transcription	Primary B cells from cord blood	blood
20	chr2:233612000-233622400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr2:233612000-233623000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:233612000-233631000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:233612000-233634000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:233612000-233634000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:233612000-233640000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:233612000-233644600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:233612200-233622200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:233612200-233622600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:233612200-233622800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:233612200-233623000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:233612200-233623400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:233612200-233623800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:233612200-233633800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:233612200-233634000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:233612200-233634400	Strong transcription	Fetal Thymus	thymus
36	chr2:233612200-233638400	Strong transcription	Placenta	Placenta
37	chr2:233612600-233637200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:233613600-233627400	Weak transcription	Ovary	ovary
39	chr2:233613800-233635600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:233614000-233628800	Weak transcription	Fetal Brain Male	brain
41	chr2:233614000-233636800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:233614200-233627000	Weak transcription	Brain Angular Gyrus	brain
43	chr2:233614400-233622200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:233614400-233626200	Weak transcription	NHEK	skin
45	chr2:233614400-233632800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:233614600-233622200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:233614600-233622600	Strong transcription	Fetal Intestine Small	intestine
48	chr2:233614600-233643600	Weak transcription	Small Intestine	intestine
49	chr2:233615000-233626000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:233615800-233626000	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links