Variant report

Variant	rs1583342
Chromosome Location	chr11:74550956-74550957
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	chr11:74550798..74553553-chr11:74554025..74555880,2	MCF-7	breast:
2	chr11:74459165..74461202-chr11:74549654..74551938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11236269	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11605604	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12363224	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1282460	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1282461	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1282689	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1282690	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1282692	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];0.89[EUR][1000 genomes]
rs1282695	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1292895	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1297319	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1303525	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1315297	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2028343	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2028344	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2033532	0.86[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2919057	0.93[JPT][hapmap]
rs41531051	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4245439	0.84[CEU][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs471462	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs473080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs473256	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs480840	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs483615	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4944945	0.87[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap]
rs495246	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs497772	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs502225	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs505688	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs508319	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs511021	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs511890	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];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs512780	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs513137	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519741	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs527529	0.85[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs529249	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs529488	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs537054	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]
rs538502	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs543244	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs546643	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs550491	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs550869	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs550980	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs557483	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs561589	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs562265	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs565767	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs567956	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs568558	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs568758	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs571446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs573925	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs577063	0.84[EUR][1000 genomes]
rs577102	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs580142	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs590105	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs599722	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs603062	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs614832	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs616085	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs624786	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs625268	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs629573	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs641584	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs643807	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs646287	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs688665	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9444	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs997465	0.93[ASW][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.96[MKK][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	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
4	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1583342	XRRA1	cis	Artery Tibial	GTEx
rs1583342	RNF169	cis	lymphoblastoid	seeQTL
rs1583342	XRRA1	cis	parietal	SCAN
rs1583342	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs1583342	RNF169	cis	cerebellum	SCAN
rs1583342	KRTAP5-10	cis	parietal	SCAN
rs1583342	XRRA1	cis	lung	GTEx
rs1583342	XRRA1	cis	Whole Blood	GTEx
rs1583342	XRRA1	cis	Esophagus Mucosa	GTEx
rs1583342	RP11-147I3.1	cis	Thyroid	GTEx
rs1583342	XRRA1	cis	Adipose Subcutaneous	GTEx
rs1583342	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs1583342	XRRA1	cis	lymphoblastoid	seeQTL
rs1583342	XRRA1	cis	Thyroid	GTEx
rs1583342	XRRA1	cis	cerebellum	SCAN
rs1583342	XRRA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
2	chr11:74533800-74553200	Weak transcription	Fetal Heart	heart
3	chr11:74538400-74553200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:74538400-74559000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:74538400-74560000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:74538600-74554600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:74539200-74557200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:74541600-74551400	Strong transcription	Primary T cells from cord blood	blood
9	chr11:74541800-74556400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr11:74543800-74565800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:74544000-74557400	Strong transcription	Dnd41	blood
12	chr11:74544000-74557600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:74544200-74557200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:74544200-74558400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr11:74544800-74551800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:74545000-74551200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr11:74545200-74551000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:74545200-74556800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr11:74545600-74564600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr11:74545600-74568400	Strong transcription	Fetal Intestine Large	intestine
22	chr11:74545800-74551400	Strong transcription	Fetal Thymus	thymus
23	chr11:74545800-74551800	Strong transcription	Colonic Mucosa	Colon
24	chr11:74545800-74552000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:74545800-74559800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr11:74545800-74560400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:74545800-74565000	Strong transcription	Fetal Muscle Leg	muscle
28	chr11:74546000-74566800	Strong transcription	Fetal Stomach	stomach
29	chr11:74546200-74559400	Strong transcription	Fetal Lung	lung
30	chr11:74546400-74551600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:74547400-74552600	Weak transcription	Psoas Muscle	Psoas
32	chr11:74547400-74556000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:74547600-74552800	Weak transcription	NHEK	skin
34	chr11:74547600-74557600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:74547600-74571400	Weak transcription	Fetal Brain Male	brain
36	chr11:74547800-74551200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr11:74547800-74555200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:74547800-74562800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr11:74548000-74551200	Weak transcription	Brain Substantia Nigra	brain
40	chr11:74548000-74553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:74548000-74553200	Weak transcription	Spleen	Spleen
42	chr11:74548000-74555400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr11:74548000-74558200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:74548000-74560600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:74548200-74552600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:74548200-74552800	Weak transcription	Right Ventricle	heart
47	chr11:74548400-74552800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:74548400-74552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:74548400-74554000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:74548600-74552000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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