Variant report

Variant	rs10205944
Chromosome Location	chr2:11448958-11448959
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10175719	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10178332	0.94[CEU][hapmap]
rs10192593	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs10192994	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10194620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs10203916	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10210600	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs10454126	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs10929732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11694729	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap]
rs11695377	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs12692434	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs12692435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12692437	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.83[YRI][hapmap]
rs12990641	0.87[CEU][hapmap]
rs12992581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12994807	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs13015560	0.87[CEU][hapmap]
rs13017021	0.87[CEU][hapmap]
rs1562748	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs1562749	0.93[CEU][hapmap]
rs1868584	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2044758	0.93[CEU][hapmap]
rs2084577	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs2122384	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2230775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2290157	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2357996	0.93[CEU][hapmap]
rs3771109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3911110	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs4303693	0.94[CEU][hapmap]
rs4668720	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4669710	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs4669713	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs4669715	0.93[CEU][hapmap]
rs6432183	0.93[CEU][hapmap]
rs6432184	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6432186	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs6710031	0.93[CEU][hapmap]
rs6713273	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap]
rs6720821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6721445	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs6730673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs6733312	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs6736240	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6749456	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]
rs6755196	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs6755337	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs6759490	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs6760802	0.93[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap]
rs7355446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7355489	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs753770	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7558664	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs7563468	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap]
rs7563928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7568064	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7575837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7586803	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7593091	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap]
rs9287728	0.93[CEU][hapmap]
rs965665	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv962059	chr2:11447027-11450757	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv961381	chr2:11448178-11449578	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10205944	ROCK2	cis	cerebellum	SCAN
rs10205944	IAH1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11424800-11455200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:11439200-11453000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:11443800-11449400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:11444000-11449800	Weak transcription	Aorta	Aorta
5	chr2:11444000-11458600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:11444800-11454600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:11445000-11465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:11445200-11450200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr2:11445400-11460200	Weak transcription	Left Ventricle	heart
10	chr2:11445800-11449800	Weak transcription	Lung	lung
11	chr2:11446200-11453200	Weak transcription	K562	blood
12	chr2:11446800-11449800	Weak transcription	HMEC	breast
13	chr2:11447000-11449800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:11447000-11449800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:11447000-11449800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:11447000-11449800	Weak transcription	Fetal Intestine Small	intestine
17	chr2:11447000-11450200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:11447000-11450400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:11447000-11450600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:11447000-11450600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:11447000-11451400	Weak transcription	Small Intestine	intestine
22	chr2:11447000-11454400	Weak transcription	Fetal Heart	heart
23	chr2:11447000-11456000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:11447000-11459800	Weak transcription	Fetal Kidney	kidney
25	chr2:11447000-11460000	Weak transcription	Ovary	ovary
26	chr2:11447000-11460200	Weak transcription	Fetal Lung	lung
27	chr2:11447200-11449800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:11447200-11449800	Weak transcription	Liver	Liver
29	chr2:11447200-11449800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:11447200-11449800	Weak transcription	Osteobl	bone
31	chr2:11447200-11450200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:11447200-11450200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:11447200-11450800	Weak transcription	A549	lung
34	chr2:11447200-11451000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:11447200-11451000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:11447200-11452600	Weak transcription	Fetal Stomach	stomach
37	chr2:11447200-11454400	Weak transcription	HSMM	muscle
38	chr2:11447200-11454600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:11447200-11456000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:11447200-11466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:11447400-11450200	Weak transcription	NHLF	lung
42	chr2:11447400-11450400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:11447400-11451400	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:11447600-11449800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:11447600-11449800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:11447800-11450800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr2:11448000-11449400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:11448000-11454400	Weak transcription	NHDF-Ad	bronchial
49	chr2:11448000-11465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:11448200-11451400	Weak transcription	Psoas Muscle	Psoas

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