Variant report

Variant	rs1564354
Chromosome Location	chr13:95778527-95778528
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95765198..95767036-chr13:95776278..95779037,2	MCF-7	breast:
2	chr13:95752245..95755943-chr13:95774951..95780273,6	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1189423	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1189424	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1189425	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1189427	0.80[ASN][1000 genomes]
rs1189428	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1189429	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1189465	0.81[JPT][hapmap]
rs1564353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618485	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1618738	0.86[JPT][hapmap]
rs1678342	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1678363	0.81[GIH][hapmap]
rs1678371	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678394	1.00[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1729742	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1729748	1.00[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1729751	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1729761	0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1729775	0.81[GIH][hapmap]
rs1751051	0.81[JPT][hapmap]
rs1751064	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2127295	0.89[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2127296	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2478464	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619314	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2698243	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2766481	0.96[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3782956	0.97[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3825415	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5023599	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7331308	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs943290	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832688	chr13:95633193-95780198	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv533659	chr13:95757713-96042149	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv832689	chr13:95759073-95921308	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95727000-95791600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr13:95727000-95812000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr13:95728400-95778800	Weak transcription	Ovary	ovary
4	chr13:95731200-95791600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr13:95740800-95791200	Weak transcription	NHLF	lung
6	chr13:95750400-95812400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr13:95750400-95815400	Weak transcription	Fetal Intestine Large	intestine
8	chr13:95751000-95793400	Weak transcription	Fetal Kidney	kidney
9	chr13:95751600-95795600	Weak transcription	Small Intestine	intestine
10	chr13:95752000-95789000	Weak transcription	Aorta	Aorta
11	chr13:95752200-95823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr13:95752200-95844200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:95754000-95794800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr13:95754400-95782600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:95756400-95828200	Weak transcription	HSMM	muscle
16	chr13:95757600-95814400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:95758000-95791600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:95761400-95789200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:95762200-95817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:95762400-95811800	Weak transcription	K562	blood
21	chr13:95767600-95779800	Weak transcription	Fetal Lung	lung
22	chr13:95768200-95783400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:95768200-95806600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:95768200-95819000	Weak transcription	Fetal Intestine Small	intestine
25	chr13:95769000-95789400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr13:95769400-95780200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr13:95769400-95791200	Weak transcription	Esophagus	oesophagus
28	chr13:95769800-95789000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr13:95770200-95789200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr13:95771200-95780200	Weak transcription	Brain Anterior Caudate	brain
31	chr13:95771800-95780200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:95773400-95779800	Weak transcription	Lung	lung
33	chr13:95774200-95784000	Enhancers	Stomach Mucosa	stomach
34	chr13:95774400-95780600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr13:95774400-95781200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr13:95774400-95781600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr13:95774400-95788800	Weak transcription	GM12878-XiMat	blood
38	chr13:95774400-95788800	Weak transcription	NHEK	skin
39	chr13:95774600-95791200	Weak transcription	Primary T cells from cord blood	blood
40	chr13:95774600-95815800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr13:95774800-95779800	Weak transcription	HUVEC	blood vessel
42	chr13:95776400-95779800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:95776400-95780000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr13:95776600-95779800	Weak transcription	Pancreas	Pancrea
45	chr13:95776600-95780600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr13:95776600-95789400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr13:95776800-95779800	Weak transcription	Gastric	stomach
48	chr13:95776800-95785600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr13:95776800-95789400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr13:95777400-95778600	Strong transcription	Stomach Smooth Muscle	stomach

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