Variant report

Variant	rs10754958
Chromosome Location	chr2:11472537-11472538
allele	A/G
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	chr2:11472516..11476992-chr2:11482916..11485822,6	MCF-7	breast:
4	chr2:11470381..11472827-chr2:11486435..11488434,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162976	Chromatin interaction
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

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];0.92[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10495582	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
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];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs12478098	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.90[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]
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];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];0.84[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];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs1868585	0.87[CHB][hapmap]
rs1901010	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]
rs2011812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][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];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][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];0.88[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]
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];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];0.88[MKK][hapmap];1.00[TSI][hapmap]

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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10754958	ROCK2	cis	lymphoblastoid	seeQTL
rs10754958	PQLC3	cis	Thyroid	GTEx
rs10754958	PQLC3	cis	lung	GTEx
rs10754958	PQLC3	cis	Esophagus Muscularis	GTEx
rs10754958	ROCK2	cis	multi-tissue	Pritchard

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	chr2:11470400-11472600	Weak transcription	Fetal Heart	heart
14	chr2:11470400-11479800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:11470400-11481400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:11470600-11475200	Weak transcription	Osteobl	bone
17	chr2:11470800-11472600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:11470800-11473400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:11470800-11473400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:11470800-11473600	Weak transcription	K562	blood
21	chr2:11470800-11475000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:11470800-11475200	Weak transcription	NHDF-Ad	bronchial
23	chr2:11470800-11475800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:11470800-11481200	Weak transcription	Right Atrium	heart
25	chr2:11470800-11481800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:11471000-11474800	Weak transcription	Ovary	ovary
27	chr2:11471000-11481200	Weak transcription	HSMM	muscle
28	chr2:11471200-11478600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:11471200-11480400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:11471400-11473000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr2:11471400-11475800	Enhancers	Liver	Liver
32	chr2:11471600-11477000	Enhancers	HepG2	liver
33	chr2:11472000-11472600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:11472200-11473000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:11472200-11476400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:11472200-11476400	Weak transcription	Pancreas	Pancrea
37	chr2:11472200-11482800	Weak transcription	Gastric	stomach
38	chr2:11472400-11474400	ZNF genes & repeats	A549	lung

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