Variant report

Variant	rs629573
Chromosome Location	chr11:74661235-74661236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr11:74661194-74662001	GM12892	blood:	n/a	chr11:74661621-74661640
2	FOXA2	chr11:74661107-74661371	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:74661097-74661679	HepG2	liver:	n/a	n/a
4	FOXA1	chr11:74661103-74661403	HepG2	liver:	n/a	n/a
5	HCFC1	chr11:74659436-74661559	Hela-S3	cervix:	n/a	n/a
6	HEY1	chr11:74661074-74661310	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:74659549-74661409	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr11:74659841-74661614	GM19193	blood:	n/a	n/a
9	POLR2A	chr11:74659666-74663417	GM12878	blood:	n/a	n/a
10	MAZ	chr11:74659890-74661281	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:74659836-74661847	GM12892	blood:	n/a	n/a
12	POLR2A	chr11:74659778-74663158	GM18505	blood:	n/a	n/a
13	POLR2A	chr11:74659623-74661519	IMR90	lung:	n/a	n/a
14	POLR2A	chr11:74661169-74661302	HepG2	liver:	n/a	n/a
15	MAZ	chr11:74659509-74661259	IMR90	lung:	n/a	n/a
16	RELA	chr11:74659644-74661979	GM15510	blood:	n/a	n/a
17	POLR2A	chr11:74659565-74663285	GM12891	blood:	n/a	n/a
18	POLR2A	chr11:74659706-74662134	GM19099	blood:	n/a	n/a
19	HEY1	chr11:74661042-74661308	HepG2	liver:	n/a	n/a
20	SIN3A	chr11:74659616-74661276	H1-hESC	embryonic stem cell:	n/a	chr11:74660271-74660280 chr11:74659833-74659841
21	POLR2A	chr11:74660997-74661401	HepG2	liver:	n/a	n/a
22	MXI1	chr11:74659821-74661757	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:74661096-74661963	HepG2	liver:	n/a	n/a
24	MXI1	chr11:74659380-74662170	SK-N-SH	brain:	n/a	n/a
25	MXI1	chr11:74659446-74662031	IMR90	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:74659008..74661915-chr11:74699636..74702523,6	MCF-7	breast:
2	chr11:74654949..74658411-chr11:74658805..74662988,5	MCF-7	breast:
3	chr11:74459112..74461560-chr11:74659129..74661254,3	MCF-7	breast:
4	chr11:74656443..74658415-chr11:74658426..74661700,3	MCF-7	breast:
5	chr11:74659109..74661906-chr11:74698267..74701116,3	K562	blood:
6	chr11:74660462..74662157-chr11:74951131..74952954,2	K562	blood:
7	chr11:74631440..74633367-chr11:74659822..74661525,2	MCF-7	breast:
8	chr11:74658459..74662580-chr11:74698519..74701644,8	MCF-7	breast:
9	chr11:74661075..74664022-chr11:74709710..74711926,2	K562	blood:
10	chr11:74647283..74650920-chr11:74658326..74663032,5	K562	blood:

No data

Variant related genes	Relation type
XRRA1	TF binding region
ENSG00000265344	TF binding region
ENSG00000255136	Chromatin interaction
ENSG00000265344	Chromatin interaction
ENSG00000261594	Chromatin interaction
ENSG00000162139	Chromatin interaction
ENSG00000166435	Chromatin interaction
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11236269	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11605604	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12363224	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1282460	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1282461	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1282689	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282690	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282692	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282695	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1292895	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1297319	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1303525	0.81[AMR][1000 genomes]
rs1315297	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1583342	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2028343	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028344	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033532	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851136	0.83[ASN][1000 genomes]
rs2919057	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs41531051	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs471462	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs473080	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473256	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480840	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs483615	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs495246	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs497772	0.81[AMR][1000 genomes]
rs502225	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs505688	0.86[AMR][1000 genomes]
rs508319	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs511021	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511890	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512780	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs513137	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs519741	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527529	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs529249	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs529488	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537054	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs538502	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs543244	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546643	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550491	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550869	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550980	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs557483	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561589	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs562265	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565767	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs567956	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568558	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568758	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571446	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573925	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577063	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577102	0.83[AMR][1000 genomes]
rs580142	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs590105	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599722	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603062	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614832	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616085	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624786	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs625268	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs641584	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643807	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646287	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688665	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997465	0.81[AFR][1000 genomes];0.84[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs629573	XRRA1	cis	lung	GTEx
rs629573	XRRA1	cis	Esophagus Mucosa	GTEx
rs629573	XRRA1	cis	Artery Tibial	GTEx
rs629573	XRRA1	cis	Thyroid	GTEx
rs629573	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs629573	RP11-147I3.1	cis	Thyroid	GTEx
rs629573	XRRA1	cis	Whole Blood	GTEx
rs629573	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs629573	XRRA1	cis	Muscle Skeletal	GTEx
rs629573	XRRA1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74658600-74661600	Active TSS	K562	blood
2	chr11:74658800-74661600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr11:74659000-74661400	Active TSS	A549	lung
4	chr11:74659000-74661600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:74659000-74661800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:74659200-74661400	Active TSS	Fetal Intestine Small	intestine
7	chr11:74659200-74661400	Active TSS	Right Ventricle	heart
8	chr11:74659200-74661400	Active TSS	NHEK	skin
9	chr11:74659200-74661600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:74659200-74661600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:74659200-74661600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr11:74659200-74661600	Active TSS	Psoas Muscle	Psoas
13	chr11:74659200-74662200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr11:74659400-74661400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:74659400-74661400	Active TSS	Fetal Lung	lung
16	chr11:74659400-74661400	Active TSS	Fetal Muscle Leg	muscle
17	chr11:74659400-74661600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr11:74659400-74661600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:74659400-74661600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:74659400-74661600	Active TSS	Muscle Satellite Cultured Cells	--
21	chr11:74659400-74661600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:74659400-74661600	Active TSS	Colonic Mucosa	Colon
23	chr11:74659400-74661600	Active TSS	Fetal Intestine Large	intestine
24	chr11:74659400-74661600	Active TSS	Right Atrium	heart
25	chr11:74659400-74661600	Active TSS	HSMMtube	muscle
26	chr11:74659400-74661800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr11:74659400-74661800	Active TSS	H9 Cell Line	embryonic stem cell
28	chr11:74659400-74661800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr11:74659400-74661800	Active TSS	Fetal Kidney	kidney
30	chr11:74659400-74661800	Active TSS	NHLF	lung
31	chr11:74659400-74662000	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr11:74659400-74662200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr11:74659400-74662200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:74659400-74662400	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr11:74659600-74661400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:74659600-74661400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:74659600-74661400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:74659600-74661400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:74659600-74661400	Active TSS	Placenta	Placenta
40	chr11:74659600-74661400	Active TSS	Gastric	stomach
41	chr11:74659600-74661400	Active TSS	Stomach Mucosa	stomach
42	chr11:74659600-74661600	Active TSS	Aorta	Aorta
43	chr11:74659600-74661600	Active TSS	Fetal Muscle Trunk	muscle
44	chr11:74659600-74661600	Active TSS	Left Ventricle	heart
45	chr11:74659600-74661600	Active TSS	Ovary	ovary
46	chr11:74659600-74661600	Active TSS	Pancreas	Pancrea
47	chr11:74659600-74661600	Active TSS	NHDF-Ad	bronchial
48	chr11:74659600-74661800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr11:74659600-74661800	Active TSS	GM12878-XiMat	blood
50	chr11:74659800-74661600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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