Variant report

Variant	rs563731
Chromosome Location	chr11:77122469-77122470
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	chr11:77120907..77124363-chr11:77182142..77186268,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268635	Chromatin interaction
ENSG00000149269	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs11237123	1.00[JPT][hapmap]
rs11237141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11237142	0.87[ASN][1000 genomes]
rs11237148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11237150	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11237151	0.87[ASN][1000 genomes]
rs11237164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1125619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1225478	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12361757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12363707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12363842	0.87[ASN][1000 genomes]
rs12363944	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12366261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1237490	0.88[EUR][1000 genomes]
rs12794253	0.87[ASN][1000 genomes]
rs1377472	0.87[ASN][1000 genomes]
rs1597954	0.80[ASN][1000 genomes]
rs1622364	0.87[ASN][1000 genomes]
rs1670446	0.87[ASN][1000 genomes]
rs1670449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1670450	0.87[ASN][1000 genomes]
rs1670456	0.87[ASN][1000 genomes]
rs1670458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1670461	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1670462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17824184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1793468	0.87[ASN][1000 genomes]
rs1793471	0.84[ASN][1000 genomes]
rs1793472	0.87[ASN][1000 genomes]
rs1793487	0.87[ASN][1000 genomes]
rs1793490	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2154754	0.84[EUR][1000 genomes]
rs2156567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2602476	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602483	0.87[ASN][1000 genomes]
rs2602487	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2725820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2725822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2725825	0.87[ASN][1000 genomes]
rs2725828	0.84[ASN][1000 genomes]
rs3015982	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015983	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015986	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015990	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019233	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019234	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3019235	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019236	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3019249	0.89[EUR][1000 genomes]
rs3019257	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34025917	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34880271	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4375461	0.87[ASN][1000 genomes]
rs472691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs476258	0.88[EUR][1000 genomes]
rs479104	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs494289	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs503406	0.96[EUR][1000 genomes]
rs505841	0.87[EUR][1000 genomes]
rs508662	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs51500	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs520938	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs522015	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs523481	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs531638	0.88[EUR][1000 genomes]
rs535008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552323	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs557484	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs558470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs560571	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs562845	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs572485	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs576220	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs580624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs592602	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs595654	0.88[EUR][1000 genomes]
rs598801	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs644551	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649040	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs653792	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs657269	0.82[EUR][1000 genomes]
rs66518011	0.84[ASN][1000 genomes]
rs66540426	0.87[ASN][1000 genomes]
rs66728428	0.87[ASN][1000 genomes]
rs674259	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs683455	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683762	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs684793	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686068	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689108	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7934230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7949721	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs883224	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs883680	0.87[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	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77118800-77123600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr11:77120800-77123400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr11:77121000-77122600	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr11:77121000-77122600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:77121000-77122600	Flanking Active TSS	Dnd41	blood
6	chr11:77121000-77123400	Active TSS	Brain Angular Gyrus	brain
7	chr11:77121200-77122600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr11:77121200-77123000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr11:77121200-77123200	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr11:77121200-77123200	Active TSS	NHLF	lung
11	chr11:77121200-77123400	Active TSS	Brain Cingulate Gyrus	brain
12	chr11:77121400-77122800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:77121400-77123400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr11:77121400-77123400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr11:77121400-77123600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:77121600-77122600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:77121600-77122600	Flanking Active TSS	NHEK	skin
18	chr11:77121600-77123200	Active TSS	Brain Hippocampus Middle	brain
19	chr11:77121600-77123400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr11:77121600-77123400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr11:77121600-77123400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:77121800-77122600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:77121800-77123000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr11:77121800-77123400	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr11:77122000-77122600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:77122000-77122600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:77122000-77122600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:77122000-77122600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:77122000-77122600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr11:77122000-77122600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr11:77122000-77122600	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr11:77122000-77122600	Flanking Active TSS	Fetal Brain Female	brain
33	chr11:77122000-77122600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr11:77122000-77122600	Flanking Active TSS	Osteobl	bone
35	chr11:77122000-77122800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:77122000-77122800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:77122000-77122800	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr11:77122000-77122800	Flanking Active TSS	Fetal Brain Male	brain
39	chr11:77122000-77122800	Flanking Active TSS	Hela-S3	cervix
40	chr11:77122000-77123000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:77122000-77123200	Active TSS	Brain Anterior Caudate	brain
42	chr11:77122000-77123200	Active TSS	Brain Substantia Nigra	brain
43	chr11:77122000-77123400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:77122000-77123600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr11:77122200-77122600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:77122200-77122600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:77122200-77122600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr11:77122200-77122600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr11:77122200-77122600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr11:77122200-77122600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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