Variant report

Variant	rs12478098
Chromosome Location	chr2:11384518-11384519
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10168084	0.96[CEU][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10169868	0.86[AMR][1000 genomes]
rs10176416	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187981	0.86[CHB][hapmap]
rs10192483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10198045	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs10495582	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10754958	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10929725	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10929726	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10929727	0.87[CHB][hapmap]
rs10929728	0.87[CHB][hapmap]
rs11674991	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11691429	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11891012	0.83[CHB][hapmap]
rs12465116	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12470004	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12472868	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12475086	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12475627	0.92[ASN][1000 genomes]
rs12478870	0.81[EUR][1000 genomes]
rs12622447	0.87[CHB][hapmap]
rs12987956	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	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12996712	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13022598	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13030319	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13393192	0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes]
rs13397757	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs13404430	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes]
rs13423864	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes]
rs13424069	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1515219	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546597	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546598	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17366643	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17366657	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17366874	0.96[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17463896	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1868585	0.87[CHB][hapmap]
rs1901010	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2011812	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2056103	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2122383	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2176052	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2230774	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2290156	0.87[CHB][hapmap]
rs2357997	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2358007	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3206843	0.84[AMR][1000 genomes]
rs34213264	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34586031	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34623763	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34727260	0.80[EUR][1000 genomes]
rs35407012	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35432367	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35508648	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35515036	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35563401	0.84[EUR][1000 genomes]
rs36072395	0.87[AMR][1000 genomes]
rs3732103	0.87[GIH][hapmap]
rs3771106	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4477886	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4595944	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4669700	0.83[CHB][hapmap]
rs4669702	0.87[CHB][hapmap]
rs4669708	0.86[CHB][hapmap]
rs55641887	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55995833	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56243142	0.84[AMR][1000 genomes]
rs56256182	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57554471	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58263533	0.83[AMR][1000 genomes]
rs62120156	0.86[EUR][1000 genomes]
rs62121446	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62121447	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6707667	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6711793	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6716447	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716817	0.93[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6728627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6736194	0.83[CHB][hapmap]
rs6739310	0.83[CHB][hapmap]
rs6743710	0.82[CHB][hapmap]
rs6753921	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726843	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7560132	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7580593	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7581130	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7589152	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7589629	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7598032	0.81[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes]
rs7600696	0.87[AMR][1000 genomes]
rs8996	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921321	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs921322	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978906	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395022	chr2:11316915-11426380	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1013570	chr2:11321519-11405246	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv2607	chr2:11381341-11409932	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12478098	ROCK2	cis	cerebellum	SCAN
rs12478098	C2orf50	cis	parietal	SCAN
rs12478098	ROCK2	cis	parietal	SCAN
rs12478098	IAH1	cis	cerebellum	SCAN
rs12478098	PQLC3	cis	Thyroid	GTEx
rs12478098	ROCK2	cis	lymphoblastoid	seeQTL
rs12478098	ROCK2	cis	multi-tissue	Pritchard
rs12478098	PQLC3	cis	lung	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
2	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
3	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
4	chr2:11333400-11386200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:11352600-11411200	Weak transcription	Thymus	Thymus
6	chr2:11352800-11424000	Weak transcription	HSMMtube	muscle
7	chr2:11354400-11388000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:11354600-11423800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:11360400-11396400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:11361000-11397000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:11361000-11397400	Weak transcription	Left Ventricle	heart
12	chr2:11361000-11399200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:11361000-11400200	Weak transcription	Gastric	stomach
14	chr2:11361000-11410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:11361000-11411200	Weak transcription	Fetal Thymus	thymus
16	chr2:11361000-11416600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:11361200-11425600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:11361600-11396800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:11364000-11387000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:11364400-11387600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:11364400-11423800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:11364800-11397400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:11365400-11387400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:11366000-11391000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:11366400-11396800	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:11366600-11390800	Weak transcription	NHLF	lung
27	chr2:11367600-11387000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:11367600-11387000	Weak transcription	Placenta	Placenta
29	chr2:11367600-11388200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:11367800-11387000	Weak transcription	Dnd41	blood
31	chr2:11368200-11387000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:11368400-11394400	Weak transcription	Brain Angular Gyrus	brain
33	chr2:11369600-11388000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:11370400-11394200	Weak transcription	Fetal Lung	lung
35	chr2:11372600-11397200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:11372600-11423800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:11373400-11387200	Weak transcription	Fetal Intestine Small	intestine
38	chr2:11375400-11390600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:11375600-11387200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:11376000-11387000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:11376200-11387200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:11376200-11410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:11376800-11387000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:11376800-11387000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:11376800-11387600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:11376800-11394200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:11376800-11395000	Weak transcription	Fetal Heart	heart
48	chr2:11376800-11399000	Weak transcription	Brain Anterior Caudate	brain
49	chr2:11378800-11428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:11379800-11387200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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