Variant report

Variant	rs1239691
Chromosome Location	chr13:51162133-51162134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51148960..51151212-chr13:51161969..51163948,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1239681	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1239682	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1239683	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239684	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239685	0.91[ASN][1000 genomes]
rs1239686	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239687	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239688	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239689	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239690	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239692	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239693	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239694	0.91[ASN][1000 genomes]
rs1239695	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1239696	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1239701	0.91[ASN][1000 genomes]
rs1239702	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1239703	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1239704	0.87[ASN][1000 genomes]
rs1239705	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1239707	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1270717	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1271766	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2794469	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs706598	0.85[ASN][1000 genomes]
rs706601	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs706602	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs770383	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs770384	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs770385	0.85[EUR][1000 genomes]
rs770386	0.85[EUR][1000 genomes]
rs770387	0.84[ASN][1000 genomes]
rs770388	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs770390	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs770391	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs770392	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs770393	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs770394	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs770395	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs770396	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs947380	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs947381	0.91[ASN][1000 genomes]
rs947382	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs947383	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9596313	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51149600-51162200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:51150400-51167400	Weak transcription	HepG2	liver
3	chr13:51151200-51169600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr13:51156200-51167600	Weak transcription	Fetal Kidney	kidney
5	chr13:51158400-51162200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:51158400-51164000	Enhancers	Fetal Muscle Leg	muscle
7	chr13:51159400-51168000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:51159400-51168000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr13:51159400-51170600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:51159600-51165000	Enhancers	Fetal Heart	heart
11	chr13:51159600-51168400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr13:51160000-51163600	Enhancers	Placenta	Placenta
13	chr13:51160000-51166600	Enhancers	Fetal Thymus	thymus
14	chr13:51160000-51168000	Weak transcription	Thymus	Thymus
15	chr13:51160200-51174000	Enhancers	Primary B cells from peripheral blood	blood
16	chr13:51160400-51163400	Weak transcription	Adipose Nuclei	Adipose
17	chr13:51160600-51164000	Enhancers	Primary B cells from cord blood	blood
18	chr13:51160800-51168000	Enhancers	Dnd41	blood
19	chr13:51161000-51162600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr13:51161000-51163800	Enhancers	NHDF-Ad	bronchial
21	chr13:51161000-51164200	Enhancers	Primary hematopoietic stem cells	blood
22	chr13:51161200-51162600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr13:51161200-51165000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:51161200-51165400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr13:51161200-51166000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr13:51161400-51162200	Weak transcription	Fetal Lung	lung
27	chr13:51161400-51164800	Enhancers	Osteobl	bone
28	chr13:51161400-51167600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:51161400-51168000	Weak transcription	Fetal Intestine Small	intestine
30	chr13:51161600-51163600	Enhancers	NH-A	brain
31	chr13:51161800-51162200	Enhancers	Lung	lung
32	chr13:51161800-51162200	Enhancers	Spleen	Spleen
33	chr13:51161800-51162400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr13:51161800-51162400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:51161800-51162800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr13:51161800-51163800	Enhancers	Right Atrium	heart
37	chr13:51161800-51164000	Enhancers	GM12878-XiMat	blood
38	chr13:51161800-51164600	Enhancers	HSMMtube	muscle
39	chr13:51162000-51162200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr13:51162000-51163200	Enhancers	Fetal Muscle Trunk	muscle
41	chr13:51162000-51163600	Enhancers	Left Ventricle	heart
42	chr13:51162000-51163600	Enhancers	Right Ventricle	heart
43	chr13:51162000-51164800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:51162000-51165400	Enhancers	HSMM	muscle
45	chr13:51162000-51168000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr13:51162000-51168800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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