Variant report

Variant	rs12992581
Chromosome Location	chr2:11456373-11456374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11450066..11451573-chr2:11455094..11457155,2	MCF-7	breast:
2	chr2:11452123..11453873-chr2:11454228..11456636,2	MCF-7	breast:
3	chr2:11449416..11451875-chr2:11454672..11457949,3	K562	blood:
4	chr2:11455012..11457129-chr2:11460561..11462468,2	K562	blood:
5	chr2:11454425..11456556-chr2:11460014..11461725,2	MCF-7	breast:
6	chr2:11455012..11458402-chr2:11459652..11462468,3	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10169455	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175719	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10183296	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10192593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10194620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10203916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10205944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10210600	0.85[AMR][1000 genomes]
rs10929732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs11681822	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11694729	0.86[YRI][hapmap]
rs11695377	0.81[YRI][hapmap]
rs12477052	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12692434	0.84[YRI][hapmap];0.87[AMR][1000 genomes]
rs12692435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692437	0.86[YRI][hapmap]
rs12994807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002722	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014721	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1562748	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs1868584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2060635	0.83[AMR][1000 genomes]
rs2084577	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs2122384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2290157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2357995	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4353615	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669706	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4669709	0.87[AMR][1000 genomes]
rs4669710	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs4669711	0.87[AMR][1000 genomes]
rs4669713	0.81[YRI][hapmap]
rs55714132	0.94[ASN][1000 genomes]
rs57082519	0.94[ASN][1000 genomes]
rs57282107	0.94[ASN][1000 genomes]
rs57339546	0.94[ASN][1000 genomes]
rs57861284	0.94[ASN][1000 genomes]
rs58007526	1.00[ASN][1000 genomes]
rs58275781	0.85[ASN][1000 genomes]
rs59194382	1.00[ASN][1000 genomes]
rs59211791	0.94[ASN][1000 genomes]
rs59266229	0.94[ASN][1000 genomes]
rs59883361	1.00[ASN][1000 genomes]
rs60643530	0.94[ASN][1000 genomes]
rs61575329	1.00[ASN][1000 genomes]
rs62118012	0.87[AMR][1000 genomes]
rs6432184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6432185	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6432186	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs6713273	0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs6713382	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6720821	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6730673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6732258	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6733312	0.87[YRI][hapmap];0.87[AMR][1000 genomes]
rs6736240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749456	0.80[YRI][hapmap];0.87[AMR][1000 genomes]
rs6753875	0.84[AFR][1000 genomes]
rs6755196	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs6755337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759490	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785499	0.94[ASN][1000 genomes]
rs7355446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7355489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73915106	0.94[ASN][1000 genomes]
rs73915107	0.94[ASN][1000 genomes]
rs73915109	0.94[ASN][1000 genomes]
rs73915134	0.94[ASN][1000 genomes]
rs73915135	0.94[ASN][1000 genomes]
rs73915140	0.94[ASN][1000 genomes]
rs73915144	1.00[ASN][1000 genomes]
rs73915151	1.00[ASN][1000 genomes]
rs73915152	1.00[ASN][1000 genomes]
rs73915154	1.00[ASN][1000 genomes]
rs73915155	1.00[ASN][1000 genomes]
rs73915156	1.00[ASN][1000 genomes]
rs73915158	1.00[ASN][1000 genomes]
rs73915159	1.00[ASN][1000 genomes]
rs73915389	0.84[ASN][1000 genomes]
rs73915390	0.88[ASN][1000 genomes]
rs73915394	0.94[ASN][1000 genomes]
rs73915395	0.94[ASN][1000 genomes]
rs73915396	0.94[ASN][1000 genomes]
rs73917504	0.94[ASN][1000 genomes]
rs73917507	0.94[ASN][1000 genomes]
rs73917508	0.94[ASN][1000 genomes]
rs73917511	0.94[ASN][1000 genomes]
rs753770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7558664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7563468	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7568064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7575837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7593091	0.86[YRI][hapmap]
rs7593966	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9712182	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12992581	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs12992581	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11444000-11458600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:11445000-11465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:11445400-11460200	Weak transcription	Left Ventricle	heart
4	chr2:11447000-11459800	Weak transcription	Fetal Kidney	kidney
5	chr2:11447000-11460000	Weak transcription	Ovary	ovary
6	chr2:11447000-11460200	Weak transcription	Fetal Lung	lung
7	chr2:11447200-11466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:11448000-11465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:11449600-11458800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:11450600-11466600	Weak transcription	NHLF	lung
11	chr2:11451200-11460000	Weak transcription	Adipose Nuclei	Adipose
12	chr2:11451400-11461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:11451600-11467000	Weak transcription	Primary B cells from cord blood	blood
14	chr2:11451800-11466000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:11452000-11460000	Weak transcription	Psoas Muscle	Psoas
16	chr2:11452000-11466000	Weak transcription	Small Intestine	intestine
17	chr2:11454400-11457000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:11454400-11469800	Weak transcription	Fetal Brain Male	brain
19	chr2:11454600-11466000	Weak transcription	Brain Angular Gyrus	brain
20	chr2:11455000-11460000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:11455000-11460000	Weak transcription	K562	blood
22	chr2:11455000-11462800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:11455000-11469200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:11455200-11466600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:11455600-11465400	Weak transcription	NHDF-Ad	bronchial
26	chr2:11456000-11456400	Weak transcription	Fetal Intestine Small	intestine
27	chr2:11456000-11456800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:11456000-11457400	Enhancers	Colon Smooth Muscle	Colon
29	chr2:11456000-11457600	Enhancers	Liver	Liver
30	chr2:11456000-11457600	Enhancers	A549	lung
31	chr2:11456000-11469400	Weak transcription	HSMM	muscle
32	chr2:11456200-11456600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:11456200-11456800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:11456200-11457600	Enhancers	HepG2	liver
35	chr2:11456200-11460000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:11456200-11460200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:11456200-11460200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:11456200-11460200	Weak transcription	Fetal Heart	heart
39	chr2:11456200-11466000	Weak transcription	Brain Inferior Temporal Lobe	brain

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