Variant report

Variant	rs590105
Chromosome Location	chr11:74624011-74624012
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74617868..74619628-chr11:74622578..74625095,2	K562	blood:

Variant related genes	Relation type
ENSG00000166435	Chromatin interaction

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

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

rs_ID	r²[population]
rs11236269	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1282460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.85[ASN][1000 genomes]
rs1282689	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282690	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1282692	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];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1282695	0.92[ASN][1000 genomes]
rs1292895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1297319	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1315297	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1583342	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]
rs2028343	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028344	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2033532	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2919057	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs41531051	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4245439	0.81[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap]
rs471462	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs473080	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs473256	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480840	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[ASN][1000 genomes]
rs495246	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs497772	0.82[EUR][1000 genomes]
rs502225	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs505688	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs508319	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511021	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511890	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];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512780	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs519741	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs527529	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529249	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529488	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs537054	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]
rs538502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs543244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs546643	0.94[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550869	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550980	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs557483	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561589	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs562265	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs567956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568558	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568758	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]
rs571446	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs573925	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577063	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577102	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs580142	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs599722	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603062	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs616085	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs624786	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625268	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs643807	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs646287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688665	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs997465	0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs590105	XRRA1	cis	parietal	SCAN
rs590105	RP11-147I3.1	cis	Thyroid	GTEx
rs590105	KRTAP5-10	cis	parietal	SCAN
rs590105	XRRA1	cis	Adipose Subcutaneous	GTEx
rs590105	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs590105	XRRA1	cis	Muscle Skeletal	GTEx
rs590105	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs590105	XRRA1	cis	lymphoblastoid	seeQTL
rs590105	XRRA1	cis	cerebellum	SCAN
rs590105	XRRA1	cis	lung	GTEx
rs590105	XRRA1	cis	Thyroid	GTEx
rs590105	XRRA1	cis	Whole Blood	GTEx
rs590105	RNF169	cis	cerebellum	SCAN
rs590105	XRRA1	cis	Artery Tibial	GTEx
rs590105	XRRA1	cis	Nerve Tibial	GTEx
rs590105	RNF169	cis	lymphoblastoid	seeQTL
rs590105	XRRA1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74587400-74629600	Weak transcription	Gastric	stomach
2	chr11:74588400-74630600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:74588400-74636000	Weak transcription	NHLF	lung
4	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
5	chr11:74598400-74629600	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:74606600-74626400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
8	chr11:74612400-74629600	Weak transcription	NHDF-Ad	bronchial
9	chr11:74612800-74634000	Weak transcription	Psoas Muscle	Psoas
10	chr11:74613400-74632600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:74613600-74627800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:74613800-74628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:74613800-74637400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr11:74614600-74633600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:74615000-74629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:74615000-74629600	Weak transcription	NH-A	brain
17	chr11:74615000-74636200	Weak transcription	A549	lung
18	chr11:74615200-74632600	Strong transcription	Liver	Liver
19	chr11:74615200-74637200	Weak transcription	HMEC	breast
20	chr11:74615400-74626400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:74615600-74626600	Strong transcription	Dnd41	blood
22	chr11:74615800-74633600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr11:74615800-74644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr11:74616000-74634200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr11:74616000-74634800	Strong transcription	Fetal Intestine Large	intestine
26	chr11:74616200-74626800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:74616200-74634000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:74616400-74633600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr11:74616400-74634400	Strong transcription	Primary T cells from cord blood	blood
30	chr11:74616400-74646000	Weak transcription	Spleen	Spleen
31	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
32	chr11:74616600-74629200	Weak transcription	Fetal Thymus	thymus
33	chr11:74616600-74632600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr11:74616600-74632600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr11:74617000-74631800	Weak transcription	HUVEC	blood vessel
36	chr11:74617200-74624800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:74617200-74630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr11:74617200-74635200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:74617400-74626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:74617400-74627200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:74617400-74629600	Weak transcription	Lung	lung
42	chr11:74617400-74648200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:74618000-74624400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr11:74618000-74627200	Strong transcription	Brain Anterior Caudate	brain
45	chr11:74618000-74659600	Weak transcription	Esophagus	oesophagus
46	chr11:74618400-74628000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr11:74618400-74653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:74618600-74625800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:74619000-74629600	Weak transcription	Aorta	Aorta
50	chr11:74619200-74629200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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