Variant report

Variant	rs28695994
Chromosome Location	chr4:75096452-75096453
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	chr4:75091219..75093823-chr4:75093870..75096715,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10009707	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10013212	0.84[EUR][1000 genomes]
rs10017409	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10017417	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10018373	0.86[EUR][1000 genomes]
rs10019396	0.83[EUR][1000 genomes]
rs10028285	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1037824	0.85[EUR][1000 genomes]
rs10433673	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938112	0.83[EUR][1000 genomes]
rs11724468	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11731340	0.81[EUR][1000 genomes]
rs11737662	0.88[EUR][1000 genomes]
rs11945418	0.83[EUR][1000 genomes]
rs1246575	0.92[EUR][1000 genomes]
rs1246577	0.93[EUR][1000 genomes]
rs1246578	0.88[EUR][1000 genomes]
rs1246579	0.88[EUR][1000 genomes]
rs1246580	0.90[EUR][1000 genomes]
rs1246582	0.93[EUR][1000 genomes]
rs1246584	0.93[EUR][1000 genomes]
rs1246586	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1246587	0.93[EUR][1000 genomes]
rs1246588	0.93[EUR][1000 genomes]
rs1246590	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1246591	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1246594	0.85[EUR][1000 genomes]
rs1246597	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12500697	0.90[EUR][1000 genomes]
rs1265327	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13116896	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142241	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1371796	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371797	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1380561	0.90[EUR][1000 genomes]
rs1460016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460017	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16850862	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16850883	0.85[EUR][1000 genomes]
rs1964526	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2045616	0.85[EUR][1000 genomes]
rs2045617	0.85[EUR][1000 genomes]
rs2045618	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061508	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2367555	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2367745	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28378517	0.81[EUR][1000 genomes]
rs28436705	0.84[EUR][1000 genomes]
rs28539097	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28592249	0.81[EUR][1000 genomes]
rs28644493	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4371587	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4577545	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4694184	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488440	0.91[EUR][1000 genomes]
rs536541	0.86[EUR][1000 genomes]
rs565831	0.86[EUR][1000 genomes]
rs62312513	0.88[EUR][1000 genomes]
rs62312515	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6446983	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446984	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6446985	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6811214	0.84[EUR][1000 genomes]
rs6814880	0.85[EUR][1000 genomes]
rs6819605	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6820992	0.85[EUR][1000 genomes]
rs6835734	0.85[EUR][1000 genomes]
rs6854203	0.89[EUR][1000 genomes]
rs6858809	0.81[EUR][1000 genomes]
rs7659389	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7665105	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7672588	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7676371	0.86[EUR][1000 genomes]
rs7678292	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7681137	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7681763	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7681912	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683181	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992393	0.90[EUR][1000 genomes]
rs9997788	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv594683	chr4:75013441-75106485	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594684	chr4:75015750-75106485	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1009099	chr4:75089233-75726206	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75056800-75096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:75067800-75097000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:75068400-75096600	Weak transcription	Adipose Nuclei	Adipose
4	chr4:75072200-75099200	Weak transcription	Ovary	ovary
5	chr4:75080600-75109600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:75085400-75102600	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:75086200-75117600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:75090200-75097000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:75090400-75102200	Weak transcription	Pancreas	Pancrea
10	chr4:75091600-75096600	Weak transcription	Left Ventricle	heart
11	chr4:75091800-75103200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:75093000-75105000	Weak transcription	Lung	lung
13	chr4:75093000-75117400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:75093200-75100600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:75093600-75101000	Weak transcription	Liver	Liver
16	chr4:75095000-75097200	Enhancers	NH-A	brain
17	chr4:75095000-75097400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr4:75095000-75098400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:75095600-75096600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:75096000-75096800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:75096000-75097600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr4:75096200-75097400	Enhancers	Stomach Mucosa	stomach
23	chr4:75096200-75097600	Enhancers	NHLF	lung
24	chr4:75096400-75096600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr4:75096400-75096600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr4:75096400-75096600	Active TSS	A549	lung
27	chr4:75096400-75096600	Flanking Active TSS	Hela-S3	cervix
28	chr4:75096400-75096600	Enhancers	HSMM	muscle
29	chr4:75096400-75096600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr4:75096400-75096600	Enhancers	NHEK	skin
31	chr4:75096400-75096800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:75096400-75096800	Enhancers	Duodenum Mucosa	Duodenum
33	chr4:75096400-75096800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr4:75096400-75097000	Enhancers	GM12878-XiMat	blood
35	chr4:75096400-75097000	Enhancers	K562	blood
36	chr4:75096400-75097200	Flanking Active TSS	HUVEC	blood vessel
37	chr4:75096400-75097400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:75096400-75097400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:75096400-75097400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:75096400-75097400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:75096400-75097400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:75096400-75097400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:75096400-75097400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr4:75096400-75097400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:75096400-75097400	Enhancers	HMEC	breast
46	chr4:75096400-75097400	Flanking Active TSS	HSMMtube	muscle
47	chr4:75096400-75097400	Flanking Active TSS	NHDF-Ad	bronchial
48	chr4:75096400-75097400	Flanking Active TSS	Osteobl	bone

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