Variant report

Variant	rs568758
Chromosome Location	chr11:74681409-74681410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74680895..74682724-chr11:74692938..74695695,2	K562	blood:
2	chr11:74681321..74682156-chr21:39620602..39621471,2	MCF-7	breast:
3	chr11:74664840..74666882-chr11:74679624..74681629,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11236269	0.92[ASN][1000 genomes]
rs11605604	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12363224	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1282460	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.81[ASN][1000 genomes]
rs1282689	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282690	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1282692	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];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1282695	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1292895	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1297319	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1315297	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1583342	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]
rs2028343	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033532	0.96[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2851136	0.85[ASN][1000 genomes]
rs2919057	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs41531051	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4245439	0.81[CEU][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap]
rs471462	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs473080	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs473256	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs480840	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs495246	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs502225	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs505688	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs508319	0.90[ASN][1000 genomes]
rs511021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511890	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];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512780	0.81[CEU][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs513137	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs519741	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527529	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs529249	0.92[ASN][1000 genomes]
rs529488	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537054	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]
rs538502	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs543244	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs546643	0.98[ASN][1000 genomes]
rs550491	0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs550869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550980	0.82[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs557483	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs561589	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs562265	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568558	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs571446	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs573925	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs577063	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs577102	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs580142	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs590105	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs599722	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603062	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs614832	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs616085	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624786	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625268	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641584	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643807	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs646287	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs688665	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444	0.96[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs997465	0.83[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs568758	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs568758	RNF169	cis	lymphoblastoid	seeQTL
rs568758	RP11-147I3.1	cis	Thyroid	GTEx
rs568758	XRRA1	cis	Esophagus Mucosa	GTEx
rs568758	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs568758	XRRA1	cis	Artery Tibial	GTEx
rs568758	XRRA1	cis	Thyroid	GTEx
rs568758	XRRA1	cis	Muscle Skeletal	GTEx
rs568758	XRRA1	cis	Adipose Subcutaneous	GTEx
rs568758	XRRA1	cis	lung	GTEx
rs568758	XRRA1	cis	Whole Blood	GTEx
rs568758	XRRA1	cis	cerebellum	SCAN
rs568758	XRRA1	cis	parietal	SCAN
rs568758	KRTAP5-10	cis	parietal	SCAN
rs568758	RNF169	cis	cerebellum	SCAN
rs568758	XRRA1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74661200-74688600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:74661600-74686000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:74661800-74699200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:74661800-74699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:74662000-74682200	Weak transcription	Aorta	Aorta
6	chr11:74662000-74682800	Weak transcription	Colonic Mucosa	Colon
7	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
8	chr11:74662400-74691400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:74662600-74682800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:74662600-74686000	Weak transcription	Fetal Brain Male	brain
11	chr11:74662800-74682200	Weak transcription	Lung	lung
12	chr11:74665600-74686000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:74667600-74689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:74667800-74683200	Weak transcription	Small Intestine	intestine
15	chr11:74667800-74692200	Strong transcription	Dnd41	blood
16	chr11:74668600-74682400	Weak transcription	Right Ventricle	heart
17	chr11:74671000-74682200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr11:74671600-74686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:74671800-74682000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr11:74672000-74682000	Weak transcription	Brain Anterior Caudate	brain
21	chr11:74672000-74692000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:74672400-74690600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:74673400-74682000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr11:74673400-74683200	Weak transcription	Gastric	stomach
25	chr11:74673400-74683200	Weak transcription	Pancreas	Pancrea
26	chr11:74673400-74686000	Weak transcription	Psoas Muscle	Psoas
27	chr11:74673400-74691000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:74673400-74694400	Weak transcription	Stomach Mucosa	stomach
29	chr11:74673800-74691600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr11:74674000-74692200	Strong transcription	GM12878-XiMat	blood
31	chr11:74674400-74690600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr11:74674600-74692000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:74674600-74692000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:74674800-74692400	Strong transcription	Fetal Thymus	thymus
35	chr11:74675000-74692000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:74675000-74692200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr11:74675200-74691400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr11:74675200-74691400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:74675200-74692200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:74675400-74689600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:74675600-74685000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:74675600-74686000	Weak transcription	Fetal Heart	heart
43	chr11:74675600-74687000	Strong transcription	Liver	Liver
44	chr11:74675600-74692000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:74675600-74692200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:74675600-74699400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr11:74675800-74681600	Strong transcription	Fetal Intestine Large	intestine
48	chr11:74675800-74692200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr11:74676000-74682000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr11:74676000-74682200	Weak transcription	Ovary	ovary

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