Variant report

Variant	rs2742514
Chromosome Location	chr11:8942670-8942671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8708580..8711045-chr11:8941082..8943163,2	K562	blood:
2	chr11:8941546..8948177-chr11:8950032..8955141,6	MCF-7	breast:
3	chr11:8940894..8943078-chr11:8949203..8951550,2	K562	blood:
4	chr11:8940620..8943003-chr11:8946457..8949397,2	MCF-7	breast:
5	chr11:8934819..8937365-chr11:8941717..8944369,2	K562	blood:
6	chr11:8932894..8935848-chr11:8939704..8942877,3	MCF-7	breast:
7	chr11:8940894..8943173-chr11:8949726..8951550,2	K562	blood:

Variant related genes	Relation type
ENSG00000166452	Chromatin interaction
ENSG00000176029	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10219366	0.85[AMR][1000 genomes]
rs1025438	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10734639	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10743094	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10769974	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10769976	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10769977	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10840150	0.83[AMR][1000 genomes]
rs10840151	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840153	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840154	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840155	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840156	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11042128	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042129	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042131	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1136966	0.82[MEX][hapmap]
rs12296005	0.85[JPT][hapmap]
rs12785559	0.81[ASN][1000 genomes]
rs12786377	0.81[ASN][1000 genomes]
rs12790020	0.81[ASN][1000 genomes]
rs12794962	0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12798311	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12805109	0.81[ASN][1000 genomes]
rs1347016	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985026	0.81[ASN][1000 genomes]
rs2016844	0.91[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2043218	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2056903	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2116510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2116511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2163625	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2246878	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247038	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252102	0.83[ASN][1000 genomes]
rs2316523	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2316541	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568034	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2568042	0.91[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs2568047	0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2568069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568074	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568075	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568077	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568079	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568081	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568086	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2568087	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568088	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653556	0.87[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs2653565	0.91[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs2653587	0.83[ASN][1000 genomes]
rs2653590	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2653594	0.89[EUR][1000 genomes]
rs2653597	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2653601	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2653611	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742473	0.81[ASN][1000 genomes]
rs2742486	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742489	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742493	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742494	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2742495	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742496	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[ASN][1000 genomes]
rs2742497	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742502	0.82[MEX][hapmap]
rs2742504	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742505	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742512	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742513	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742521	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs3751063	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3751065	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3751066	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3751068	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3763911	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3763912	0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4370967	0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs4909951	0.91[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4910313	0.81[ASN][1000 genomes]
rs7106152	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7124403	0.81[ASN][1000 genomes]
rs72851596	0.93[ASN][1000 genomes]
rs72852790	0.93[ASN][1000 genomes]
rs72853712	0.93[ASN][1000 genomes]
rs7932377	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7940895	0.86[ASN][1000 genomes]
rs7942026	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7951226	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs909464	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9300096	0.91[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs982273	0.87[CEU][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2742514	C11orf17	cis	multi-tissue	Pritchard
rs2742514	MRVI1	cis	cerebellum	SCAN
rs2742514	C11orf17	cis	lymphoblastoid	seeQTL
rs2742514	TMEM9B	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
2	chr11:8933600-8944000	Weak transcription	Pancreas	Pancrea
3	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:8934200-8948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:8936000-8942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:8936200-8945800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr11:8936400-8946000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:8936400-8946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
10	chr11:8936600-8945000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:8936600-8945800	Weak transcription	Stomach Mucosa	stomach
12	chr11:8936600-8946600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:8936600-8948600	Strong transcription	Fetal Thymus	thymus
14	chr11:8936600-8949000	Strong transcription	Fetal Stomach	stomach
15	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:8936800-8947000	Strong transcription	Dnd41	blood
17	chr11:8936800-8947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:8937000-8947600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:8937000-8948200	Strong transcription	Fetal Brain Female	brain
20	chr11:8937200-8945000	Strong transcription	Brain Angular Gyrus	brain
21	chr11:8937200-8947400	Strong transcription	Thymus	Thymus
22	chr11:8937600-8944800	Strong transcription	Hela-S3	cervix
23	chr11:8937800-8947400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:8938000-8943000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:8938000-8943200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr11:8938000-8944200	Strong transcription	HUVEC	blood vessel
27	chr11:8938000-8944600	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr11:8938000-8944800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr11:8938000-8944800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr11:8938000-8944800	Strong transcription	Fetal Intestine Large	intestine
31	chr11:8938000-8945000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr11:8938000-8945000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr11:8938000-8945800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:8938000-8946400	Strong transcription	Brain Hippocampus Middle	brain
35	chr11:8938000-8946600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:8938000-8946800	Strong transcription	Liver	Liver
37	chr11:8938000-8947400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:8938000-8947600	Strong transcription	Brain Cingulate Gyrus	brain
39	chr11:8938200-8943000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr11:8938200-8943200	Strong transcription	Primary T cells from cord blood	blood
41	chr11:8938200-8944800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr11:8938200-8947000	Strong transcription	Brain Anterior Caudate	brain
43	chr11:8938200-8947200	Strong transcription	Brain Germinal Matrix	brain
44	chr11:8938400-8945000	Strong transcription	Brain Substantia Nigra	brain
45	chr11:8938400-8945000	Strong transcription	Right Ventricle	heart
46	chr11:8938400-8946800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr11:8938600-8944800	Strong transcription	Placenta	Placenta
48	chr11:8938600-8945000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:8938600-8945200	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr11:8938600-8946600	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links