Variant report

Variant	rs12987956
Chromosome Location	chr2:11312181-11312182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10168084	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10176416	0.87[EUR][1000 genomes]
rs10192483	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs10198045	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs10495582	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs10754958	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap]
rs10929725	0.81[ASN][1000 genomes]
rs10929726	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11674991	0.88[EUR][1000 genomes]
rs11680818	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]
rs11683786	0.80[MEX][hapmap]
rs11691429	0.91[EUR][1000 genomes]
rs12465116	0.90[EUR][1000 genomes]
rs12470004	0.96[CEU][hapmap];0.91[CHB][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12470798	0.82[ASW][hapmap];1.00[YRI][hapmap]
rs12472868	0.87[EUR][1000 genomes]
rs12475086	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs12478098	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs12996399	0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13002429	1.00[YRI][hapmap]
rs13013938	0.83[AMR][1000 genomes]
rs13018466	0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs13022598	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes]
rs13030319	0.81[EUR][1000 genomes]
rs13393192	0.81[CEU][hapmap]
rs13397757	0.81[CEU][hapmap]
rs13404430	0.93[GIH][hapmap]
rs13424069	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs1515219	0.82[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs1546597	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs1546598	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes]
rs17366322	1.00[YRI][hapmap]
rs17366643	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap]
rs17366657	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs17366874	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs17463896	0.82[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs1901010	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap]
rs2011812	0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.81[ASN][1000 genomes]
rs2056103	0.91[CHB][hapmap]
rs2122383	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs2176052	0.82[EUR][1000 genomes]
rs2271622	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs2357997	0.88[EUR][1000 genomes]
rs33985535	0.82[EUR][1000 genomes]
rs34213264	0.87[EUR][1000 genomes]
rs34586031	0.81[EUR][1000 genomes]
rs34623763	0.81[EUR][1000 genomes]
rs34727260	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35432367	0.89[EUR][1000 genomes]
rs35508648	0.86[EUR][1000 genomes]
rs35515036	0.86[EUR][1000 genomes]
rs35563401	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35898907	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3732103	0.87[CHB][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap]
rs3771106	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]
rs3856468	0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs3951242	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4477886	0.86[CHB][hapmap]
rs55641887	0.89[EUR][1000 genomes]
rs55995833	0.90[EUR][1000 genomes]
rs56256182	0.86[EUR][1000 genomes]
rs57554471	0.88[EUR][1000 genomes]
rs62120153	0.81[EUR][1000 genomes]
rs62120155	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62120156	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62121446	0.89[EUR][1000 genomes]
rs62121447	0.89[EUR][1000 genomes]
rs6707667	0.81[EUR][1000 genomes]
rs6711793	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6716447	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs6716817	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap]
rs6728627	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs6753921	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs726843	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes]
rs7560132	0.89[EUR][1000 genomes]
rs7580593	0.91[EUR][1000 genomes]
rs7589152	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[EUR][1000 genomes]
rs7589629	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs7598032	0.93[GIH][hapmap]
rs8996	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs921321	0.81[ASN][1000 genomes]
rs921322	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs978906	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12987956	C2orf50	cis	parietal	SCAN
rs12987956	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs12987956	ROCK2	cis	cerebellum	SCAN
rs12987956	PQLC3	cis	Esophagus Muscularis	GTEx
rs12987956	IAH1	cis	cerebellum	SCAN
rs12987956	PQLC3	cis	Thyroid	GTEx
rs12987956	ROCK2	cis	parietal	SCAN
rs12987956	PQLC3	cis	lung	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11329400	Weak transcription	Gastric	stomach
2	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
3	chr2:11296400-11314200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:11296400-11314800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:11296400-11315200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:11296400-11315200	Weak transcription	Brain Substantia Nigra	brain
7	chr2:11296400-11315400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:11296400-11318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:11296600-11315200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:11296600-11315200	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:11296600-11315200	Weak transcription	NHDF-Ad	bronchial
12	chr2:11296600-11319200	Weak transcription	Fetal Lung	lung
13	chr2:11296800-11315000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:11296800-11315200	Weak transcription	Brain Anterior Caudate	brain
15	chr2:11296800-11318200	Weak transcription	A549	lung
16	chr2:11296800-11379800	Weak transcription	Small Intestine	intestine
17	chr2:11297600-11315200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
19	chr2:11297800-11315200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:11298200-11315400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:11298200-11317600	Weak transcription	Fetal Brain Male	brain
22	chr2:11299200-11357000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:11300200-11315400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:11300600-11315400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:11301400-11330400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:11301600-11315200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:11301800-11315400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:11301800-11324600	Weak transcription	Primary B cells from cord blood	blood
29	chr2:11302000-11315200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:11302400-11315200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:11302400-11315400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:11302400-11321400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:11302400-11326200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:11302400-11335600	Weak transcription	Lung	lung
35	chr2:11303800-11314600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:11304200-11315200	Weak transcription	Primary T cells from cord blood	blood
37	chr2:11304200-11317800	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:11304400-11314400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:11304400-11315200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:11304400-11315200	Weak transcription	HMEC	breast
41	chr2:11304400-11315200	Weak transcription	HSMM	muscle
42	chr2:11304400-11315400	Weak transcription	Left Ventricle	heart
43	chr2:11304400-11315400	Weak transcription	HSMMtube	muscle
44	chr2:11304400-11317800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:11304400-11321400	Weak transcription	Esophagus	oesophagus
46	chr2:11304400-11321400	Weak transcription	Fetal Stomach	stomach
47	chr2:11304400-11325200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:11304400-11326400	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:11304400-11329200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:11304800-11315400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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