Variant report

Variant	rs10929732
Chromosome Location	chr2:11483492-11483493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11446328..11449302-chr2:11482839..11485533,2	MCF-7	breast:
2	chr2:11482372..11487550-chr2:11525654..11531960,9	MCF-7	breast:
3	chr2:11373041..11376680-chr2:11481459..11486793,6	MCF-7	breast:
4	chr2:11481545..11486787-chr2:11491378..11496218,8	MCF-7	breast:
5	chr2:11483291..11485571-chr2:11604286..11606431,2	MCF-7	breast:
6	chr2:11292941..11297094-chr2:11480820..11486254,6	MCF-7	breast:
7	chr2:11483049..11486978-chr2:11530307..11533471,4	MCF-7	breast:
8	chr2:11482371..11485428-chr2:11534025..11537515,3	K562	blood:
9	chr2:10951194..10953015-chr2:11483398..11486312,2	MCF-7	breast:
10	chr1:53017681..53018376-chr2:11483294..11483986,2	Hela-S3	cervix:
11	chr2:11482684..11486384-chr2:11678704..11682899,6	MCF-7	breast:
12	chr2:11294308..11297184-chr2:11482767..11485221,3	K562	blood:
13	chr2:11482129..11485059-chr2:11681594..11684381,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226961	Chromatin interaction
ENSG00000231403	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000207267	Chromatin interaction
ENSG00000264010	Chromatin interaction
ENSG00000230154	Chromatin interaction
ENSG00000134318	Chromatin interaction
ENSG00000162976	Chromatin interaction
ENSG00000224177	Chromatin interaction
ENSG00000169016	Chromatin interaction
ENSG00000143870	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10173492	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10175719	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs10192593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10192994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10194620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10203916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10205944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11694729	0.86[YRI][hapmap]
rs11695377	0.81[YRI][hapmap]
rs12467103	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692434	0.84[YRI][hapmap]
rs12692435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs12692437	0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs12992581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs12994807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs13016386	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1562748	0.81[YRI][hapmap]
rs1868584	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1901011	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2084577	0.81[YRI][hapmap]
rs2122384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs2230775	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2290157	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3771109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4668720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs4668721	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4669710	0.81[YRI][hapmap]
rs4669712	0.87[AMR][1000 genomes]
rs4669713	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs57404216	1.00[ASN][1000 genomes]
rs58258043	1.00[ASN][1000 genomes]
rs6432184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6432185	0.83[AMR][1000 genomes]
rs6432186	0.81[YRI][hapmap]
rs6713273	0.86[YRI][hapmap]
rs6720821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6730673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6733312	0.87[YRI][hapmap]
rs6736240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs6743977	0.89[ASN][1000 genomes]
rs6749456	0.80[YRI][hapmap]
rs6755196	0.81[YRI][hapmap]
rs6755337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs6759490	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7355446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7355489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs73915164	1.00[ASN][1000 genomes]
rs73915165	1.00[ASN][1000 genomes]
rs73915167	1.00[ASN][1000 genomes]
rs753770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7558664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs7563468	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs7563928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7568064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs7575837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.83[AMR][1000 genomes]
rs7586803	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7593091	0.86[YRI][hapmap]
rs9712182	0.83[AMR][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
rs10929732	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs10929732	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11479800-11485400	Active TSS	GM12878-XiMat	blood
2	chr2:11480000-11485800	Active TSS	Aorta	Aorta
3	chr2:11481000-11483800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:11481000-11483800	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr2:11481000-11483800	Flanking Active TSS	Liver	Liver
6	chr2:11481000-11485200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:11481000-11485600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:11481000-11485600	Active TSS	NHLF	lung
9	chr2:11481000-11485800	Active TSS	Ovary	ovary
10	chr2:11481200-11483600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:11481200-11484400	Bivalent/Poised TSS	HepG2	liver
12	chr2:11481200-11484600	Active TSS	Right Atrium	heart
13	chr2:11481200-11485600	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr2:11481600-11485400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:11481600-11485400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:11481600-11485600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:11481600-11485600	Active TSS	Brain Germinal Matrix	brain
18	chr2:11481600-11485800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:11481800-11483800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:11481800-11483800	Active TSS	Fetal Brain Female	brain
21	chr2:11481800-11485200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:11481800-11485600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:11481800-11485600	Active TSS	Fetal Intestine Large	intestine
24	chr2:11481800-11485600	Active TSS	NHDF-Ad	bronchial
25	chr2:11481800-11485800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:11481800-11486000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:11482000-11485400	Active TSS	A549	lung
28	chr2:11482000-11485400	Active TSS	Hela-S3	cervix
29	chr2:11482000-11485800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr2:11482000-11486000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:11482000-11486000	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr2:11482200-11483600	Flanking Active TSS	Dnd41	blood
33	chr2:11482200-11483600	Flanking Active TSS	HUVEC	blood vessel
34	chr2:11482200-11483800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:11482200-11484200	Active TSS	Fetal Brain Male	brain
36	chr2:11482200-11485200	Active TSS	Stomach Smooth Muscle	stomach
37	chr2:11482200-11485400	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr2:11482200-11485400	Active TSS	Colon Smooth Muscle	Colon
39	chr2:11482200-11485400	Active TSS	HSMMtube	muscle
40	chr2:11482200-11485600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:11482200-11485600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:11482200-11485600	Active TSS	Rectal Smooth Muscle	rectum
43	chr2:11482200-11485800	Active TSS	Fetal Muscle Trunk	muscle
44	chr2:11482200-11485800	Active TSS	Psoas Muscle	Psoas
45	chr2:11482400-11483600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr2:11482400-11483800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr2:11482400-11484000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:11482400-11485200	Active TSS	Muscle Satellite Cultured Cells	--
49	chr2:11482400-11485200	Active TSS	HMEC	breast
50	chr2:11482400-11485400	Active TSS	Fetal Muscle Leg	muscle

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