Variant report

Variant	rs473256
Chromosome Location	chr11:74631702-74631703
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74631440..74633367-chr11:74659822..74661525,2	MCF-7	breast:
2	chr11:74624254..74626945-chr11:74627904..74632353,5	K562	blood:

Variant related genes	Relation type
ENSG00000166435	Chromatin interaction
ENSG00000241170	Chromatin interaction
ENSG00000118363	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs11236269	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1282460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1282689	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282690	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1282692	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];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1282695	0.92[ASN][1000 genomes]
rs1292895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1297319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1315297	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1583342	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]
rs2028343	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028344	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2033532	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2919057	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs41531051	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4245439	0.84[CEU][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs471462	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs473080	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs480840	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[ASN][1000 genomes]
rs495246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs497772	0.82[EUR][1000 genomes]
rs502225	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs505688	0.86[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs508319	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs511021	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511890	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];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512780	0.86[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs519741	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs527529	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529249	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529488	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs537054	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]
rs538502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs543244	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs546643	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550869	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550980	0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs557483	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561589	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs562265	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs567956	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568758	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]
rs571446	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs573925	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577063	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577102	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs580142	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs590105	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]
rs599722	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs616085	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs624786	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs643807	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs646287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688665	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs997465	0.80[ASW][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]

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	nsv972046	chr11:74629931-74632251	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs473256	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs473256	XRRA1	cis	Artery Tibial	GTEx
rs473256	XRRA1	cis	lymphoblastoid	seeQTL
rs473256	XRRA1	cis	Adipose Subcutaneous	GTEx
rs473256	XRRA1	cis	lung	GTEx
rs473256	XRRA1	cis	multi-tissue	Pritchard
rs473256	XRRA1	cis	Whole Blood	GTEx
rs473256	XRRA1	cis	Thyroid	GTEx
rs473256	RNF169	cis	multi-tissue	Pritchard
rs473256	XRRA1	cis	Muscle Skeletal	GTEx
rs473256	XRRA1	cis	Esophagus Mucosa	GTEx
rs473256	RP11-147I3.1	cis	Thyroid	GTEx
rs473256	RNF169	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74588400-74636000	Weak transcription	NHLF	lung
2	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
3	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
4	chr11:74612800-74634000	Weak transcription	Psoas Muscle	Psoas
5	chr11:74613400-74632600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:74613800-74637400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:74614600-74633600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:74615000-74636200	Weak transcription	A549	lung
9	chr11:74615200-74632600	Strong transcription	Liver	Liver
10	chr11:74615200-74637200	Weak transcription	HMEC	breast
11	chr11:74615800-74633600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:74615800-74644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr11:74616000-74634200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr11:74616000-74634800	Strong transcription	Fetal Intestine Large	intestine
15	chr11:74616200-74634000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:74616400-74633600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr11:74616400-74634400	Strong transcription	Primary T cells from cord blood	blood
18	chr11:74616400-74646000	Weak transcription	Spleen	Spleen
19	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
20	chr11:74616600-74632600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:74616600-74632600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:74617000-74631800	Weak transcription	HUVEC	blood vessel
23	chr11:74617200-74635200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:74617400-74648200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:74618000-74659600	Weak transcription	Esophagus	oesophagus
26	chr11:74618400-74653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:74619200-74639800	Weak transcription	K562	blood
28	chr11:74620000-74646200	Weak transcription	Right Ventricle	heart
29	chr11:74620400-74659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:74621200-74634800	Strong transcription	Primary B cells from cord blood	blood
31	chr11:74622400-74633000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:74622800-74633000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:74623800-74632400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:74624200-74643200	Weak transcription	HSMMtube	muscle
35	chr11:74624600-74632400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:74624600-74632800	Strong transcription	Thymus	Thymus
37	chr11:74625400-74633000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:74625400-74634200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:74625600-74632200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:74625600-74633000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:74625800-74633000	Strong transcription	Ovary	ovary
42	chr11:74625800-74633400	Strong transcription	Fetal Muscle Leg	muscle
43	chr11:74626000-74632200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:74626000-74632400	Strong transcription	Adipose Nuclei	Adipose
45	chr11:74626200-74632800	Strong transcription	Placenta	Placenta
46	chr11:74626200-74633000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:74626400-74632200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:74626800-74632600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:74627600-74632600	Strong transcription	Brain Anterior Caudate	brain
50	chr11:74627600-74632600	Strong transcription	Left Ventricle	heart

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