Variant report

Variant	rs2762509
Chromosome Location	chr1:95025421-95025422
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	chr1:95007807..95010270-chr1:95025313..95026976,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1041041	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1041042	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165158	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146473	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1146474	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1146476	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1146477	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1146480	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1146481	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1146482	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1146484	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1146485	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146487	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1146489	0.87[EUR][1000 genomes]
rs1146491	0.87[EUR][1000 genomes]
rs1146492	0.86[EUR][1000 genomes]
rs1146494	0.86[EUR][1000 genomes]
rs1146496	0.87[EUR][1000 genomes]
rs1146498	0.87[EUR][1000 genomes]
rs1146500	0.90[EUR][1000 genomes]
rs1146501	0.91[EUR][1000 genomes]
rs11485356	0.87[EUR][1000 genomes]
rs12075529	0.87[EUR][1000 genomes]
rs12089040	0.82[ASN][1000 genomes]
rs12354005	0.87[EUR][1000 genomes]
rs1245215	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1303132	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1303134	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1303135	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1303137	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1303138	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1303139	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1324217	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1578535	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1772904	0.84[EUR][1000 genomes]
rs1772911	0.87[EUR][1000 genomes]
rs1778205	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1778206	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1778207	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1778208	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1778223	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1778226	0.87[EUR][1000 genomes]
rs2093843	0.87[EUR][1000 genomes]
rs2794475	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2794476	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794479	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2971946	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2971947	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2985287	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2996292	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668501	0.83[EUR][1000 genomes]
rs68169338	0.97[EUR][1000 genomes]
rs927633	0.84[EUR][1000 genomes]
rs927634	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs927635	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs927636	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs968661	0.84[EUR][1000 genomes]
rs968662	0.83[EUR][1000 genomes]

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	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95019000-95028200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:95019000-95028200	Weak transcription	Pancreas	Pancrea
3	chr1:95020400-95028200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:95020600-95025600	Weak transcription	HSMM	muscle
5	chr1:95020600-95028000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:95021000-95025600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:95021400-95027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:95023800-95025600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:95025200-95025800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:95025200-95026000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:95025200-95026000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:95025200-95026000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:95025200-95026000	Enhancers	HMEC	breast
14	chr1:95025200-95026000	Enhancers	HSMMtube	muscle
15	chr1:95025200-95026200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:95025200-95026200	Enhancers	Hela-S3	cervix
17	chr1:95025400-95025600	Enhancers	Ovary	ovary
18	chr1:95025400-95025800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:95025400-95025800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:95025400-95025800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:95025400-95025800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:95025400-95025800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:95025400-95025800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:95025400-95025800	Enhancers	Esophagus	oesophagus
25	chr1:95025400-95025800	Enhancers	NHLF	lung
26	chr1:95025400-95026000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:95025400-95026000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:95025400-95026000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:95025400-95026000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:95025400-95026000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:95025400-95026000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:95025400-95026000	Enhancers	Fetal Intestine Large	intestine
33	chr1:95025400-95026000	Enhancers	Stomach Mucosa	stomach
34	chr1:95025400-95026000	Enhancers	NHEK	skin
35	chr1:95025400-95026200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:95025400-95026200	Enhancers	HepG2	liver
37	chr1:95025400-95027200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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