Variant report

Variant	rs10167277
Chromosome Location	chr2:11366000-11366001
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11358381..11360784-chr2:11365018..11367149,2	K562	blood:
2	chr2:11365381..11369172-chr2:11380510..11384403,4	K562	blood:
3	chr2:11365433..11366937-chr2:11373686..11375238,2	MCF-7	breast:
4	chr2:11358381..11364018-chr2:11364236..11368158,7	K562	blood:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction
ENSG00000207267	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10168084	0.86[CHB][hapmap]
rs10169868	1.00[ASN][1000 genomes]
rs10180914	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10181567	0.94[ASN][1000 genomes]
rs10187981	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10204503	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10208872	0.84[CEU][hapmap]
rs10929727	0.81[CEU][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10929728	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1129976	0.88[ASN][1000 genomes]
rs11676201	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11683010	0.99[ASN][1000 genomes]
rs11891012	0.95[JPT][hapmap]
rs11891877	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12469980	0.84[ASN][1000 genomes]
rs12476188	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12618325	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12622447	0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap]
rs13017010	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13393192	0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13397757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13404430	0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13423864	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs17366874	0.86[CHB][hapmap]
rs1868585	0.81[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[ASN][1000 genomes]
rs2271621	0.88[ASN][1000 genomes]
rs2290156	0.81[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.90[ASN][1000 genomes]
rs3206843	0.87[ASN][1000 genomes]
rs34554628	0.87[ASN][1000 genomes]
rs36072395	0.92[ASN][1000 genomes]
rs3732103	0.82[CHD][hapmap]
rs4669700	0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs4669702	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4669708	0.87[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs56243142	0.90[ASN][1000 genomes]
rs58263533	0.92[ASN][1000 genomes]
rs6705170	0.86[JPT][hapmap]
rs6736194	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs6739310	0.95[JPT][hapmap]
rs6743710	0.94[JPT][hapmap]
rs7581184	0.84[CEU][hapmap]
rs7589629	0.81[CHB][hapmap]
rs7598032	0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7600696	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395022	chr2:11316915-11426380	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1013570	chr2:11321519-11405246	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10167277	C2orf50	cis	parietal	SCAN
rs10167277	ROCK2	cis	multi-tissue	Pritchard
rs10167277	PDIA6	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
2	chr2:11296800-11379800	Weak transcription	Small Intestine	intestine
3	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
4	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
5	chr2:11315800-11367400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:11320800-11377000	Strong transcription	HepG2	liver
7	chr2:11328800-11367600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:11329200-11369200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:11333400-11386200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:11337000-11367400	Weak transcription	Brain Angular Gyrus	brain
11	chr2:11338400-11367400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:11338600-11373400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:11339800-11382600	Weak transcription	Esophagus	oesophagus
14	chr2:11340600-11369400	Weak transcription	Colonic Mucosa	Colon
15	chr2:11341600-11384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:11344400-11368400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:11346800-11366400	Strong transcription	HSMM	muscle
18	chr2:11352600-11411200	Weak transcription	Thymus	Thymus
19	chr2:11352800-11424000	Weak transcription	HSMMtube	muscle
20	chr2:11353200-11374800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:11354200-11367400	Weak transcription	Brain Anterior Caudate	brain
22	chr2:11354200-11376400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:11354400-11382600	Weak transcription	Ovary	ovary
24	chr2:11354400-11388000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:11354600-11369800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:11354600-11423800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:11355200-11379800	Weak transcription	Psoas Muscle	Psoas
28	chr2:11355400-11379800	Weak transcription	NHEK	skin
29	chr2:11355800-11367400	Weak transcription	Brain Substantia Nigra	brain
30	chr2:11355800-11376200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:11356000-11366800	Weak transcription	GM12878-XiMat	blood
32	chr2:11356400-11367600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:11356400-11371800	Weak transcription	Primary T cells from cord blood	blood
34	chr2:11356800-11367600	Weak transcription	Fetal Brain Female	brain
35	chr2:11357000-11366400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:11357000-11377400	Weak transcription	Brain Germinal Matrix	brain
37	chr2:11357800-11379800	Weak transcription	HMEC	breast
38	chr2:11358800-11367800	Weak transcription	HUVEC	blood vessel
39	chr2:11359000-11382000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:11359200-11366800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:11360400-11396400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:11360800-11375200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:11360800-11382800	Weak transcription	Spleen	Spleen
44	chr2:11361000-11367200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:11361000-11369800	Weak transcription	Lung	lung
46	chr2:11361000-11372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:11361000-11372200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:11361000-11372200	Weak transcription	Fetal Stomach	stomach
49	chr2:11361000-11374800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:11361000-11378000	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links