Variant report

Variant	rs565767
Chromosome Location	chr11:74522371-74522372
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74458235..74460336-chr11:74520344..74522892,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11236269	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12363224	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1282460	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1282461	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1282690	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1282695	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1303525	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1315297	0.81[AMR][1000 genomes]
rs1583342	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2033532	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs41531051	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs471462	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs473080	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs480840	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs483615	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs497772	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs502225	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs505688	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs508319	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs512780	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs513137	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519741	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs527529	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs529249	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs538502	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs543244	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs546643	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs550491	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs557483	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs561589	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs567956	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs568558	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs571446	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs577102	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs580142	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs625268	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs629573	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs643807	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9444	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
7	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs565767	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74494800-74530600	Weak transcription	NH-A	brain
2	chr11:74496200-74533000	Weak transcription	Fetal Brain Male	brain
3	chr11:74502600-74527800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:74502800-74545600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:74503000-74522600	Weak transcription	NHLF	lung
6	chr11:74503000-74528400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:74503000-74529400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:74503000-74530200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:74503000-74530600	Weak transcription	HSMMtube	muscle
10	chr11:74503000-74531600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:74503000-74533000	Weak transcription	Right Ventricle	heart
12	chr11:74503200-74524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:74503200-74528600	Weak transcription	Lung	lung
14	chr11:74503200-74533000	Weak transcription	Gastric	stomach
15	chr11:74503200-74537800	Weak transcription	Pancreas	Pancrea
16	chr11:74503800-74529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:74504200-74528600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:74504400-74522800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:74504400-74531600	Weak transcription	HMEC	breast
20	chr11:74504400-74534600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr11:74504600-74523200	Weak transcription	Hela-S3	cervix
22	chr11:74505400-74527600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:74506200-74523800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:74506600-74522400	Weak transcription	Liver	Liver
25	chr11:74507000-74530200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:74508200-74523400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:74508200-74523600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:74508200-74529000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:74509000-74523000	Weak transcription	Fetal Stomach	stomach
30	chr11:74509000-74527800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:74509000-74528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:74509200-74530000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:74509200-74531000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:74509400-74524600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:74509400-74530000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr11:74509600-74533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:74509800-74534600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:74510400-74528000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:74512800-74522800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:74515400-74528600	Weak transcription	Right Atrium	heart
41	chr11:74515400-74533000	Weak transcription	Esophagus	oesophagus
42	chr11:74515600-74523400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr11:74515800-74527800	Weak transcription	NHEK	skin
44	chr11:74517600-74526800	Weak transcription	Fetal Heart	heart
45	chr11:74518200-74524400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:74518400-74530000	Weak transcription	A549	lung
47	chr11:74518400-74530600	Weak transcription	Psoas Muscle	Psoas
48	chr11:74518600-74522400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:74518600-74522800	Weak transcription	GM12878-XiMat	blood
50	chr11:74518600-74527000	Weak transcription	K562	blood

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