Variant report

Variant	rs2011812
Chromosome Location	chr2:11340198-11340199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11292794..11295094-chr2:11339407..11341727,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10168084	0.80[CEU][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10169868	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10176416	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10187981	0.86[CHB][hapmap]
rs10192483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10198045	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs10495582	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10754958	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap]
rs10929725	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929726	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10929727	0.87[CHB][hapmap]
rs10929728	0.87[CHB][hapmap]
rs11674991	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11680818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11691429	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11891012	0.83[CHB][hapmap]
rs12465116	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12470004	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12472868	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12475086	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12475627	0.86[ASN][1000 genomes]
rs12478098	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12622447	0.87[CHB][hapmap]
rs12987956	0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.81[ASN][1000 genomes]
rs12996399	0.81[YRI][hapmap]
rs12996712	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13013938	0.81[EUR][1000 genomes]
rs13018466	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs13022598	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13030319	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13393192	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13397757	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13404430	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13423864	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13424069	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1515219	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1546597	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1546598	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17366643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17366657	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17366874	0.81[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17463896	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1868585	0.87[CHB][hapmap]
rs1901010	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap]
rs2056103	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2122383	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2176052	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2230774	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290156	0.87[CHB][hapmap]
rs2357997	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3206843	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34213264	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34586031	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34623763	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35432367	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35508648	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35515036	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36072395	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3732103	0.84[GIH][hapmap]
rs3771106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3856468	0.81[CEU][hapmap]
rs4477886	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4595944	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4669700	0.83[CHB][hapmap]
rs4669702	0.87[CHB][hapmap]
rs4669708	0.86[CHB][hapmap]
rs55641887	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs55995833	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56243142	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56256182	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57554471	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58263533	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62120155	0.87[EUR][1000 genomes]
rs62121446	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62121447	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6707667	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6711793	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6716447	0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6716817	0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs6728627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6736194	0.83[CHB][hapmap];0.80[GIH][hapmap]
rs6739310	0.83[CHB][hapmap]
rs6743710	0.82[CHB][hapmap]
rs6753921	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs726843	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7560132	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7580593	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7581130	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7589152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7589629	0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7598032	0.81[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7600696	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8996	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs921321	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921322	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs978906	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[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	nsv1012083	chr2:11316299-11350604	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	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
3	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2011812	PQLC3	cis	lung	GTEx
rs2011812	PQLC3	cis	Thyroid	GTEx
rs2011812	ROCK2	cis	lymphoblastoid	seeQTL
rs2011812	PDIA6	cis	parietal	SCAN
rs2011812	PQLC3	cis	Esophagus Muscularis	GTEx
rs2011812	IAH1	cis	cerebellum	SCAN
rs2011812	IAH1	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr2:11299200-11357000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
6	chr2:11314600-11364200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:11315800-11340400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:11315800-11367400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:11316200-11344400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:11316200-11354200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:11316400-11351800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:11318600-11359200	Weak transcription	Fetal Heart	heart
13	chr2:11319000-11364200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:11320800-11377000	Strong transcription	HepG2	liver
15	chr2:11325600-11341000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:11326000-11356600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:11327200-11343400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:11327600-11344400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:11327800-11344200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:11328000-11342600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:11328800-11342600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:11328800-11367600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:11329000-11342600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:11329000-11343200	Strong transcription	NHDF-Ad	bronchial
25	chr2:11329000-11343800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:11329200-11342200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:11329200-11342600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:11329200-11343600	Strong transcription	Dnd41	blood
29	chr2:11329200-11364400	Strong transcription	Liver	Liver
30	chr2:11329200-11369200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:11329400-11342000	Strong transcription	Fetal Lung	lung
32	chr2:11329400-11342400	Strong transcription	Osteobl	bone
33	chr2:11329400-11343400	Strong transcription	HSMM	muscle
34	chr2:11330200-11353400	Weak transcription	Gastric	stomach
35	chr2:11330400-11343200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:11331200-11341800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:11331200-11342400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:11332200-11342400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:11332400-11357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr2:11332600-11343200	Strong transcription	Hela-S3	cervix
41	chr2:11333400-11347400	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:11333400-11386200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:11333600-11352200	Weak transcription	Psoas Muscle	Psoas
44	chr2:11333800-11342200	Weak transcription	NHEK	skin
45	chr2:11333800-11353400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:11334000-11343400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:11334400-11363600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:11334600-11344000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:11334800-11342200	Strong transcription	A549	lung
50	chr2:11334800-11342600	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links