Variant report

Variant	rs1678395
Chromosome Location	chr13:95765954-95765955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95765198..95767036-chr13:95776278..95779037,2	MCF-7	breast:
2	chr13:95763899..95767263-chr13:95780210..95781935,3	MCF-7	breast:
3	chr13:95751186..95754744-chr13:95765427..95767632,4	MCF-7	breast:
4	chr13:95751490..95755868-chr13:95765298..95769920,8	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1189430	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1189431	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1189432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1189433	0.80[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs1189434	0.86[CHD][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs1189435	0.80[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs1189436	0.80[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs1189437	0.80[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs1189438	0.86[CHD][hapmap]
rs1189439	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs1189442	0.86[CHB][hapmap]
rs1189443	0.86[CHB][hapmap]
rs1189444	0.86[CHB][hapmap]
rs1189451	0.90[CHD][hapmap]
rs1189452	0.90[CHD][hapmap]
rs1189461	0.90[CHD][hapmap]
rs1189462	0.90[CHD][hapmap]
rs1189466	0.90[CHD][hapmap]
rs1612388	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1630901	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1678339	0.90[CHD][hapmap]
rs1678340	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678341	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1678351	0.83[CHD][hapmap]
rs1678353	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678362	0.86[CHD][hapmap]
rs1678365	0.90[CHD][hapmap]
rs1678387	0.90[CHD][hapmap]
rs1678409	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1729745	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1729747	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1729752	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1729773	0.86[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1751031	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1751033	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1751036	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1751037	0.90[CHD][hapmap]
rs1751043	0.90[CHD][hapmap]
rs1751052	0.86[CHD][hapmap]
rs1751055	0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1751056	0.82[EUR][1000 genomes]
rs1751057	0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1751060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1751061	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2619312	0.89[CHD][hapmap]
rs2766475	0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs2950957	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4773840	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs931111	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs943289	0.83[CHD][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:65 , 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	chr13:95727800-95767800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr13:95728400-95778800	Weak transcription	Ovary	ovary
5	chr13:95728600-95776000	Weak transcription	Gastric	stomach
6	chr13:95731200-95791600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr13:95740600-95772200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr13:95740800-95791200	Weak transcription	NHLF	lung
9	chr13:95741600-95772600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr13:95750400-95812400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr13:95750400-95815400	Weak transcription	Fetal Intestine Large	intestine
12	chr13:95751000-95793400	Weak transcription	Fetal Kidney	kidney
13	chr13:95751400-95777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:95751600-95795600	Weak transcription	Small Intestine	intestine
15	chr13:95752000-95789000	Weak transcription	Aorta	Aorta
16	chr13:95752200-95823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr13:95752200-95844200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr13:95753400-95775400	Weak transcription	HSMMtube	muscle
19	chr13:95753600-95767400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:95753600-95772600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:95754000-95766800	Weak transcription	Osteobl	bone
22	chr13:95754000-95777200	Weak transcription	NHDF-Ad	bronchial
23	chr13:95754000-95794800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:95754400-95768000	Weak transcription	NH-A	brain
25	chr13:95754400-95782600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr13:95755000-95774200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr13:95755400-95776400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:95756400-95828200	Weak transcription	HSMM	muscle
29	chr13:95756600-95766400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:95757600-95772800	Weak transcription	Lung	lung
31	chr13:95757600-95814400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr13:95758000-95766600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:95758000-95791600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr13:95758200-95769200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:95758200-95774000	Weak transcription	Primary T cells from cord blood	blood
36	chr13:95758400-95772800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr13:95758600-95769200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:95760400-95766600	Weak transcription	Stomach Mucosa	stomach
39	chr13:95761400-95766800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr13:95761400-95789200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr13:95761600-95769000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:95761600-95774000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr13:95762200-95817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr13:95762400-95774000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr13:95762400-95811800	Weak transcription	K562	blood
46	chr13:95763000-95774000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:95763600-95766800	Weak transcription	NHEK	skin
48	chr13:95763600-95769000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:95764400-95767800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr13:95764400-95768400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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