Variant report

Variant	rs562265
Chromosome Location	chr11:74661110-74661111
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr11:74661107-74661371	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:74661097-74661679	HepG2	liver:	n/a	n/a
3	FOXA1	chr11:74661103-74661403	HepG2	liver:	n/a	n/a
4	HA-E2F1	chr11:74659835-74661150	MCF-7	breast:	n/a	chr11:74661006-74661018 chr11:74660277-74660286
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	EBF1	chr11:74660979-74661233	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:74659666-74663417	GM12878	blood:	n/a	n/a
11	MAZ	chr11:74659890-74661281	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:74659836-74661847	GM12892	blood:	n/a	n/a
13	POLR2A	chr11:74659778-74663158	GM18505	blood:	n/a	n/a
14	POLR2A	chr11:74659623-74661519	IMR90	lung:	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	UBTF	chr11:74660998-74661164	K562	blood:	n/a	n/a
24	CTCF	chr11:74660960-74661110	AG04449	skin:	n/a	n/a
25	POLR2A	chr11:74661096-74661963	HepG2	liver:	n/a	n/a
26	SMC3	chr11:74661046-74661163	GM12878	blood:	n/a	n/a
27	WRNIP1	chr11:74659703-74661132	GM12878	blood:	n/a	n/a
28	MXI1	chr11:74659380-74662170	SK-N-SH	brain:	n/a	n/a
29	TBL1XR1	chr11:74661061-74661148	K562	blood:	n/a	n/a
30	CTCF	chr11:74661020-74661170	RPTEC	kidney:	n/a	n/a
31	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
ENSG00000265344	Chromatin interaction
ENSG00000166435	Chromatin interaction
ENSG00000162139	Chromatin interaction
ENSG00000255136	Chromatin interaction
ENSG00000166439	Chromatin interaction
ENSG00000261594	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11236269	0.94[ASN][1000 genomes]
rs11605604	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12363224	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1282460	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1282461	0.83[ASN][1000 genomes]
rs1282689	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282690	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282692	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282695	0.98[ASN][1000 genomes]
rs1292895	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1297319	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1315297	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1583342	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2028343	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028344	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033532	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2851136	0.83[ASN][1000 genomes]
rs2919057	0.83[ASN][1000 genomes]
rs41531051	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs471462	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs473080	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473256	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480840	0.94[ASN][1000 genomes]
rs495246	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs502225	0.83[EUR][1000 genomes]
rs508319	0.92[ASN][1000 genomes]
rs511021	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511890	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513137	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs519741	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527529	0.94[ASN][1000 genomes]
rs529249	0.94[ASN][1000 genomes]
rs529488	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537054	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs538502	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs543244	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546643	1.00[ASN][1000 genomes]
rs550491	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550869	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550980	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs557483	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs567956	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568558	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568758	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571446	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573925	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577063	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs580142	0.82[EUR][1000 genomes]
rs590105	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599722	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603062	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614832	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616085	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624786	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs625268	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs629573	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641584	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643807	1.00[ASN][1000 genomes]
rs646287	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688665	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997465	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
rs562265	XRRA1	cis	Adipose Subcutaneous	GTEx
rs562265	XRRA1	cis	Whole Blood	GTEx
rs562265	XRRA1	cis	Muscle Skeletal	GTEx
rs562265	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs562265	RP11-147I3.1	cis	Thyroid	GTEx
rs562265	XRRA1	cis	Thyroid	GTEx
rs562265	XRRA1	cis	Artery Tibial	GTEx
rs562265	XRRA1	cis	Esophagus Mucosa	GTEx
rs562265	XRRA1	cis	lung	GTEx
rs562265	XRRA1	cis	Skin Sun Exposed Lower leg	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	chr11:74659200-74661200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:74659200-74661200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr11:74659200-74661200	Active TSS	Colon Smooth Muscle	Colon
9	chr11:74659200-74661200	Active TSS	Rectal Smooth Muscle	rectum
10	chr11:74659200-74661200	Active TSS	HMEC	breast
11	chr11:74659200-74661200	Active TSS	NH-A	brain
12	chr11:74659200-74661400	Active TSS	Fetal Intestine Small	intestine
13	chr11:74659200-74661400	Active TSS	Right Ventricle	heart
14	chr11:74659200-74661400	Active TSS	NHEK	skin
15	chr11:74659200-74661600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:74659200-74661600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:74659200-74661600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr11:74659200-74661600	Active TSS	Psoas Muscle	Psoas
19	chr11:74659200-74662200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr11:74659400-74661200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:74659400-74661400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:74659400-74661400	Active TSS	Fetal Lung	lung
23	chr11:74659400-74661400	Active TSS	Fetal Muscle Leg	muscle
24	chr11:74659400-74661600	Active TSS	H1 Cell Line	embryonic stem cell
25	chr11:74659400-74661600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:74659400-74661600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:74659400-74661600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr11:74659400-74661600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:74659400-74661600	Active TSS	Colonic Mucosa	Colon
30	chr11:74659400-74661600	Active TSS	Fetal Intestine Large	intestine
31	chr11:74659400-74661600	Active TSS	Right Atrium	heart
32	chr11:74659400-74661600	Active TSS	HSMMtube	muscle
33	chr11:74659400-74661800	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr11:74659400-74661800	Active TSS	H9 Cell Line	embryonic stem cell
35	chr11:74659400-74661800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr11:74659400-74661800	Active TSS	Fetal Kidney	kidney
37	chr11:74659400-74661800	Active TSS	NHLF	lung
38	chr11:74659400-74662000	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr11:74659400-74662200	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr11:74659400-74662200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:74659400-74662400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr11:74659600-74661200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr11:74659600-74661200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:74659600-74661200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:74659600-74661200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:74659600-74661200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:74659600-74661200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:74659600-74661200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:74659600-74661200	Active TSS	Esophagus	oesophagus
50	chr11:74659600-74661200	Active TSS	Lung	lung

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