Variant report

Variant	rs493001
Chromosome Location	chr11:74678203-74678204
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11236291	0.81[JPT][hapmap]
rs11236292	0.81[JPT][hapmap]
rs1125609	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs113187	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs11827626	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs12223829	0.82[EUR][1000 genomes]
rs1282668	0.85[EUR][1000 genomes]
rs1282675	0.83[EUR][1000 genomes]
rs1282677	0.83[EUR][1000 genomes]
rs1866562	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs2510692	0.84[EUR][1000 genomes]
rs476040	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs483271	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs487226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs494474	0.88[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs4944962	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs496698	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs500827	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs503855	0.88[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap]
rs503994	0.88[EUR][1000 genomes]
rs507620	0.88[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs512782	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs514534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs516287	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs517035	0.88[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs517666	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs517939	0.89[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs528800	0.81[EUR][1000 genomes]
rs535705	0.82[EUR][1000 genomes]
rs536412	0.81[JPT][hapmap]
rs544115	0.81[JPT][hapmap]
rs544891	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs545202	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs545304	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs556916	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs558303	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs559211	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs563473	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs564229	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs565377	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs571437	0.82[EUR][1000 genomes]
rs578477	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs579581	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs580042	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs592045	0.84[EUR][1000 genomes]
rs605954	0.86[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs629191	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs633824	0.87[EUR][1000 genomes]
rs639768	0.81[JPT][hapmap]
rs650130	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs655488	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs662062	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs670246	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs671544	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs673731	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs681566	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap]
rs685116	0.80[JPT][hapmap]
rs693212	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7128833	0.81[JPT][hapmap]
rs7952096	0.81[JPT][hapmap]
rs7952209	0.81[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs493001	XRRA1	cis	lymphoblastoid	seeQTL
rs493001	XRRA1	cis	parietal	SCAN
rs493001	FCHSD2	cis	cerebellum	SCAN
rs493001	PAAF1	cis	cerebellum	SCAN
rs493001	NEU3	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr11:74662000-74680800	Weak transcription	Fetal Kidney	kidney
6	chr11:74662000-74682200	Weak transcription	Aorta	Aorta
7	chr11:74662000-74682800	Weak transcription	Colonic Mucosa	Colon
8	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
9	chr11:74662400-74680600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:74662400-74691400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:74662600-74682800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:74662600-74686000	Weak transcription	Fetal Brain Male	brain
13	chr11:74662800-74682200	Weak transcription	Lung	lung
14	chr11:74663200-74680000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:74664000-74680400	Weak transcription	HMEC	breast
16	chr11:74665600-74686000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:74667600-74689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:74667800-74678400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:74667800-74683200	Weak transcription	Small Intestine	intestine
20	chr11:74667800-74692200	Strong transcription	Dnd41	blood
21	chr11:74668000-74680800	Weak transcription	Brain Angular Gyrus	brain
22	chr11:74668600-74682400	Weak transcription	Right Ventricle	heart
23	chr11:74671000-74682200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:74671600-74686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:74671800-74682000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:74672000-74682000	Weak transcription	Brain Anterior Caudate	brain
27	chr11:74672000-74692000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:74672400-74680400	Weak transcription	Fetal Brain Female	brain
29	chr11:74672400-74690600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr11:74673400-74679800	Weak transcription	HepG2	liver
31	chr11:74673400-74682000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr11:74673400-74683200	Weak transcription	Gastric	stomach
33	chr11:74673400-74683200	Weak transcription	Pancreas	Pancrea
34	chr11:74673400-74686000	Weak transcription	Psoas Muscle	Psoas
35	chr11:74673400-74691000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:74673400-74694400	Weak transcription	Stomach Mucosa	stomach
37	chr11:74673800-74679200	Strong transcription	Primary B cells from cord blood	blood
38	chr11:74673800-74691600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr11:74674000-74679800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr11:74674000-74692200	Strong transcription	GM12878-XiMat	blood
41	chr11:74674400-74678600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr11:74674400-74690600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr11:74674600-74692000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:74674600-74692000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:74674800-74678400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:74674800-74692400	Strong transcription	Fetal Thymus	thymus
47	chr11:74675000-74678400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr11:74675000-74679200	Strong transcription	Hela-S3	cervix
49	chr11:74675000-74692000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:74675000-74692200	Strong transcription	Rectal Mucosa Donor 29	rectum

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