Variant report

Variant	rs12692435
Chromosome Location	chr2:11445098-11445099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:11444324-11445318	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11434738..11436289-chr2:11444236..11445981,2	K562	blood:
2	chr2:11444512..11447438-chr2:11450182..11452688,2	K562	blood:
3	chr2:11444757..11447160-chr2:11453898..11455416,2	MCF-7	breast:
4	chr2:11443856..11445730-chr2:11445772..11448144,2	K562	blood:

Variant related genes	Relation type
ENSG00000230154	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10169455	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175719	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10183296	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10192593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10194620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10203916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10205944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10210600	0.81[AMR][1000 genomes]
rs10454126	0.81[YRI][hapmap]
rs10929729	0.83[AFR][1000 genomes]
rs10929732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs11681822	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11694729	0.86[YRI][hapmap]
rs11695377	0.85[YRI][hapmap]
rs12477052	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12692434	0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs12692437	0.86[YRI][hapmap]
rs12992581	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]
rs12994807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002722	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014721	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1562748	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs1868584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1901011	0.81[AFR][1000 genomes]
rs2084577	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs2122384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[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	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3911110	0.80[YRI][hapmap]
rs4353615	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669706	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4669709	0.83[AMR][1000 genomes]
rs4669710	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs4669711	0.83[AMR][1000 genomes]
rs4669713	0.84[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	0.83[AMR][1000 genomes]
rs6432184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6432185	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6432186	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs6713273	0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs6713382	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6720821	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6721445	0.81[YRI][hapmap]
rs6730673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6732258	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6733312	0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6736240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749456	0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs6753875	0.89[AFR][1000 genomes]
rs6755196	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs6755337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759490	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785499	0.94[ASN][1000 genomes]
rs7355446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.88[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];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[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];0.84[AFR][1000 genomes];0.88[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];0.82[AMR][1000 genomes];0.84[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];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7568064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7575837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[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	0.81[EUR][1000 genomes]
rs9712182	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[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
rs12692435	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs12692435	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11424800-11455200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:11426600-11446000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:11433200-11445600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:11433200-11446200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:11433600-11446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:11433600-11448000	Weak transcription	Right Ventricle	heart
7	chr2:11439200-11453000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:11440000-11445800	Weak transcription	Liver	Liver
9	chr2:11440200-11446000	Weak transcription	A549	lung
10	chr2:11441000-11445800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:11442200-11446000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:11442800-11447800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:11443000-11445200	Enhancers	K562	blood
14	chr2:11443200-11446400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:11443400-11446400	Enhancers	Ovary	ovary
16	chr2:11443400-11447200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:11443400-11447200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:11443600-11445600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:11443600-11445600	Weak transcription	Osteobl	bone
20	chr2:11443600-11446000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:11443600-11446600	Weak transcription	Fetal Intestine Large	intestine
22	chr2:11443600-11446800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:11443600-11447000	Enhancers	Adipose Nuclei	Adipose
24	chr2:11443800-11445600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:11443800-11449400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:11444000-11445400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:11444000-11445600	Weak transcription	Brain Angular Gyrus	brain
28	chr2:11444000-11445600	Weak transcription	Fetal Heart	heart
29	chr2:11444000-11447400	Enhancers	Colon Smooth Muscle	Colon
30	chr2:11444000-11449800	Weak transcription	Aorta	Aorta
31	chr2:11444000-11458600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:11444200-11447400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:11444400-11445200	Enhancers	Psoas Muscle	Psoas
34	chr2:11444400-11445800	Enhancers	Right Atrium	heart
35	chr2:11444400-11446000	Weak transcription	Fetal Lung	lung
36	chr2:11444400-11446400	Enhancers	Small Intestine	intestine
37	chr2:11444600-11445200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:11444600-11446800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:11444600-11447000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr2:11444600-11447800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:11444800-11445400	Enhancers	Left Ventricle	heart
42	chr2:11444800-11446000	Weak transcription	HepG2	liver
43	chr2:11444800-11447600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:11444800-11448000	Enhancers	NHDF-Ad	bronchial
45	chr2:11444800-11454600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:11445000-11445400	Weak transcription	HSMM	muscle
47	chr2:11445000-11445600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:11445000-11446000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr2:11445000-11465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links