Variant report

Variant	rs1901010
Chromosome Location	chr2:11472103-11472104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11294029..11296824-chr2:11471660..11473792,2	K562	blood:
2	chr2:11471245..11477004-chr2:11481417..11486329,8	MCF-7	breast:
3	chr2:11470381..11472827-chr2:11486435..11488434,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction
ENSG00000162976	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10168084	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs10187981	0.86[CHB][hapmap]
rs10192483	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10198045	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10495582	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs10754958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929727	0.87[CHB][hapmap]
rs10929728	0.87[CHB][hapmap]
rs11680818	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11693061	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11891012	0.83[CHB][hapmap]
rs12468344	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12470004	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs12475086	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs12478098	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]
rs12478870	0.87[AFR][1000 genomes]
rs12622447	0.87[CHB][hapmap]
rs12987956	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap]
rs12996399	0.88[CEU][hapmap]
rs13018466	0.83[CEU][hapmap]
rs13022598	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13030319	0.90[AFR][1000 genomes]
rs13393192	0.88[CEU][hapmap];0.87[CHB][hapmap]
rs13397757	0.88[CEU][hapmap]
rs13404430	0.81[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap]
rs13423864	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs13424069	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1515219	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs1546597	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1546598	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17366643	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap]
rs17366657	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17366874	0.92[CEU][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs17463896	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs1868585	0.87[CHB][hapmap]
rs2011812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap]
rs2056103	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2060634	0.86[AFR][1000 genomes]
rs2122383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2290156	0.87[CHB][hapmap]
rs34213264	0.82[AFR][1000 genomes]
rs34586031	0.90[AFR][1000 genomes]
rs34623763	0.90[AFR][1000 genomes]
rs35407012	0.93[AFR][1000 genomes]
rs35508648	0.86[AFR][1000 genomes]
rs35515036	0.86[AFR][1000 genomes]
rs3732103	0.87[GIH][hapmap]
rs3771106	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4302194	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4477886	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4669700	0.83[CHB][hapmap]
rs4669702	0.87[CHB][hapmap]
rs4669708	0.86[CHB][hapmap]
rs55641887	0.83[AFR][1000 genomes]
rs56211149	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56309145	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59048275	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716447	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs6716817	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6728627	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6736194	0.83[CHB][hapmap]
rs6739310	0.83[CHB][hapmap]
rs6743710	0.82[CHB][hapmap]
rs6753921	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs726843	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs753771	0.86[AFR][1000 genomes]
rs7557723	0.83[AFR][1000 genomes]
rs7589152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs7589629	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs7598032	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap]
rs8996	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs978906	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]

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	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	esv3423850	chr2:11469926-11472474	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1901010	ROCK2	cis	multi-tissue	Pritchard
rs1901010	ROCK2	cis	parietal	SCAN
rs1901010	ROCK2	cis	lymphoblastoid	seeQTL
rs1901010	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs1901010	ROCK2	cis	cerebellum	SCAN
rs1901010	PQLC3	cis	Esophagus Muscularis	GTEx
rs1901010	PQLC3	cis	Thyroid	GTEx
rs1901010	IAH1	cis	cerebellum	SCAN
rs1901010	PQLC3	cis	lung	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11457200-11476400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:11461000-11476400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:11464400-11475200	Weak transcription	Aorta	Aorta
4	chr2:11467000-11480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:11467400-11472600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:11467400-11481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:11467600-11481600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:11467800-11473400	Weak transcription	Adipose Nuclei	Adipose
9	chr2:11467800-11480200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:11468000-11476400	Weak transcription	Psoas Muscle	Psoas
11	chr2:11468400-11481200	Weak transcription	HUVEC	blood vessel
12	chr2:11470200-11473800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:11470400-11472200	Weak transcription	Fetal Intestine Large	intestine
14	chr2:11470400-11472400	Weak transcription	A549	lung
15	chr2:11470400-11472600	Weak transcription	Fetal Heart	heart
16	chr2:11470400-11479800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:11470400-11481400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:11470600-11475200	Weak transcription	Osteobl	bone
19	chr2:11470800-11472600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:11470800-11473400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:11470800-11473400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:11470800-11473600	Weak transcription	K562	blood
23	chr2:11470800-11475000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:11470800-11475200	Weak transcription	NHDF-Ad	bronchial
25	chr2:11470800-11475800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:11470800-11481200	Weak transcription	Right Atrium	heart
27	chr2:11470800-11481800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:11471000-11474800	Weak transcription	Ovary	ovary
29	chr2:11471000-11481200	Weak transcription	HSMM	muscle
30	chr2:11471200-11478600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:11471200-11480400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:11471400-11473000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:11471400-11475800	Enhancers	Liver	Liver
34	chr2:11471600-11477000	Enhancers	HepG2	liver
35	chr2:11471800-11472200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:11471800-11472200	Enhancers	Gastric	stomach
37	chr2:11471800-11472200	Enhancers	Pancreas	Pancrea
38	chr2:11472000-11472600	Enhancers	Skeletal Muscle Female	skeletal muscle

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