Variant report

Variant	rs12694915
Chromosome Location	chr2:233586502-233586503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10190211	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10207739	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10209575	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10933407	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10933408	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11679581	0.90[EUR][1000 genomes]
rs11684636	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11685169	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687379	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11688622	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11688691	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11689661	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11694000	0.82[TSI][hapmap]
rs11694434	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11695762	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11884228	0.84[YRI][hapmap]
rs11887276	0.82[ASW][hapmap];0.84[YRI][hapmap]
rs11887345	0.82[ASW][hapmap];0.84[YRI][hapmap]
rs11892817	0.82[ASW][hapmap];0.84[YRI][hapmap]
rs11904619	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs12052869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12328140	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12694916	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13035517	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs13383733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs13386650	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs13396293	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13401578	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs13408229	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13412034	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412513	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13424896	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs13425525	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13425918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs13429857	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1446307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289914	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292724	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs2292725	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs2293782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305139	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34063802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34832091	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35778045	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35785837	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35928329	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41266951	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56054779	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62193305	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6437073	0.86[TSI][hapmap]
rs6747479	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6751801	0.86[TSI][hapmap]
rs73005582	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7557131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564554	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9288676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9808146	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9973586	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][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
rs12694915	COPS7B	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233564000-233589000	Weak transcription	NH-A	brain
2	chr2:233564200-233596400	Weak transcription	NHLF	lung
3	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
6	chr2:233565200-233589800	Weak transcription	HMEC	breast
7	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
8	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
9	chr2:233565400-233589800	Weak transcription	Hela-S3	cervix
10	chr2:233565400-233590000	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
13	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:233569200-233589000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:233569200-233590000	Weak transcription	NHDF-Ad	bronchial
16	chr2:233569200-233615000	Weak transcription	Colonic Mucosa	Colon
17	chr2:233569400-233612800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:233569400-233615400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:233570600-233593400	Weak transcription	Aorta	Aorta
20	chr2:233571200-233593600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:233571200-233598200	Weak transcription	Fetal Kidney	kidney
22	chr2:233571200-233627400	Weak transcription	Gastric	stomach
23	chr2:233571400-233588600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:233571400-233601800	Weak transcription	Esophagus	oesophagus
25	chr2:233571600-233612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:233572200-233589000	Weak transcription	Osteobl	bone
27	chr2:233572200-233589800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:233572200-233589800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:233572200-233591600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:233572200-233593200	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:233572400-233586800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:233573600-233589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:233573800-233588600	Weak transcription	Lung	lung
34	chr2:233574200-233588800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:233574200-233589000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:233574200-233589200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:233574400-233588200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:233574400-233593400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:233575400-233586800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:233576000-233589000	Weak transcription	Brain Germinal Matrix	brain
41	chr2:233577400-233589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:233580000-233606000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:233580200-233589400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:233580200-233596000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:233580600-233604000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:233580800-233595200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:233581000-233594200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:233581200-233587600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:233581400-233589000	Weak transcription	Brain Angular Gyrus	brain
50	chr2:233581400-233589000	Weak transcription	Pancreas	Pancrea

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