Variant report

Variant	rs537054
Chromosome Location	chr11:74689372-74689373
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	chr11:74687560..74690870-chr11:74698064..74700699,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11236269	0.87[ASN][1000 genomes]
rs11605604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12363224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1282460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1282689	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1282690	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1282692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1282695	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1292895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1297319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1315297	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1583342	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2028343	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2028344	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033532	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2851136	0.88[ASN][1000 genomes]
rs2919057	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs41531051	0.88[EUR][1000 genomes]
rs4245439	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs471462	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs473080	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs473256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs480840	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs495246	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs502225	0.86[EUR][1000 genomes]
rs505688	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs508319	0.85[ASN][1000 genomes]
rs511021	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs512780	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs519741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs527529	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs529249	0.87[ASN][1000 genomes]
rs529488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs543244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs546643	0.93[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs550869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs550980	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs557483	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs561589	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs562265	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs567956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs568558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs568758	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571446	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs573925	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs577063	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577102	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs580142	0.84[EUR][1000 genomes]
rs590105	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs599722	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];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs603062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs614832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[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]
rs616085	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs624786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs625268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs629573	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs643807	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs646287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs688665	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9444	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs997465	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.89[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	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv972047	chr11:74688078-74690431	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs537054	KRTAP5-10	cis	parietal	SCAN
rs537054	XRRA1	cis	Whole Blood	GTEx
rs537054	XRRA1	cis	Esophagus Mucosa	GTEx
rs537054	XRRA1	cis	cerebellum	SCAN
rs537054	XRRA1	cis	Thyroid	GTEx
rs537054	RNF169	cis	lymphoblastoid	seeQTL
rs537054	XRRA1	cis	lymphoblastoid	seeQTL
rs537054	XRRA1	cis	Muscle Skeletal	GTEx
rs537054	XRRA1	cis	parietal	SCAN
rs537054	RNF169	cis	cerebellum	SCAN
rs537054	RNF169	cis	multi-tissue	Pritchard
rs537054	XRRA1	cis	Artery Tibial	GTEx
rs537054	XRRA1	cis	Adipose Subcutaneous	GTEx
rs537054	RP11-147I3.1	cis	Thyroid	GTEx
rs537054	XRRA1	cis	multi-tissue	Pritchard
rs537054	XRRA1	cis	lung	GTEx
rs537054	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74661800-74699200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:74661800-74699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
4	chr11:74662400-74691400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:74667800-74692200	Strong transcription	Dnd41	blood
6	chr11:74672000-74692000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:74672400-74690600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:74673400-74691000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:74673400-74694400	Weak transcription	Stomach Mucosa	stomach
10	chr11:74673800-74691600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr11:74674000-74692200	Strong transcription	GM12878-XiMat	blood
12	chr11:74674400-74690600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:74674600-74692000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:74674600-74692000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:74674800-74692400	Strong transcription	Fetal Thymus	thymus
16	chr11:74675000-74692000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:74675000-74692200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr11:74675200-74691400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr11:74675200-74691400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:74675200-74692200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:74675400-74689600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:74675600-74692000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:74675600-74692200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:74675600-74699400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:74675800-74692200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr11:74676600-74690200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:74676600-74690200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:74676600-74691800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:74676600-74691800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:74677000-74691600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:74677200-74689600	Strong transcription	Fetal Lung	lung
32	chr11:74677200-74691400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:74677200-74692400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:74677200-74692400	Strong transcription	Fetal Muscle Leg	muscle
35	chr11:74677200-74692600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:74677200-74692600	Strong transcription	Thymus	Thymus
37	chr11:74677200-74693400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:74677600-74691200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:74677600-74693800	Strong transcription	HSMM	muscle
40	chr11:74677800-74689600	Strong transcription	NHLF	lung
41	chr11:74678600-74699200	Weak transcription	Spleen	Spleen
42	chr11:74679800-74689600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr11:74679800-74691600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:74680200-74690200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:74680200-74691000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:74680200-74691200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:74680200-74692200	Strong transcription	Primary T cells from cord blood	blood
48	chr11:74680400-74691400	Strong transcription	Placenta	Placenta
49	chr11:74680400-74691600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:74680400-74692400	Strong transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links