Variant report

Variant	rs28521842
Chromosome Location	chr4:147249413-147249414
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	chr4:147246661..147249612-chr4:147255793..147257750,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10008275	0.98[ASN][1000 genomes]
rs10010528	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013722	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027135	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10032088	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11735261	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11736003	0.94[ASN][1000 genomes]
rs11737121	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11939345	0.92[ASN][1000 genomes]
rs11947781	0.88[ASN][1000 genomes]
rs17021396	0.94[ASN][1000 genomes]
rs2200474	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28625764	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4835033	0.98[ASN][1000 genomes]
rs4835292	0.86[ASN][1000 genomes]
rs4835294	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4835296	0.98[ASN][1000 genomes]
rs4835297	0.98[ASN][1000 genomes]
rs4835299	0.92[ASN][1000 genomes]
rs55798872	0.94[ASN][1000 genomes]
rs57713263	0.94[ASN][1000 genomes]
rs6846294	0.92[ASN][1000 genomes]
rs6846584	0.94[ASN][1000 genomes]
rs6846846	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857911	0.98[ASN][1000 genomes]
rs9784436	0.80[ASN][1000 genomes]
rs9784437	0.84[ASN][1000 genomes]
rs9996311	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9999381	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3451660	chr4:147225135-147271246	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3443192	chr4:147225234-147271217	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3468025	chr4:147225279-147271172	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3468026	chr4:147225279-147271172	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147201000-147249600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:147208400-147254600	Weak transcription	Gastric	stomach
3	chr4:147208600-147254800	Weak transcription	Adipose Nuclei	Adipose
4	chr4:147212800-147264200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:147215600-147254800	Weak transcription	Primary T cells from cord blood	blood
6	chr4:147229600-147257400	Weak transcription	Ovary	ovary
7	chr4:147233000-147255000	Weak transcription	Aorta	Aorta
8	chr4:147233200-147254400	Weak transcription	GM12878-XiMat	blood
9	chr4:147235200-147249600	Weak transcription	Left Ventricle	heart
10	chr4:147241800-147255200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:147241800-147284800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:147242800-147255000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:147243000-147255000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:147243200-147254800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:147244000-147251000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr4:147244200-147255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:147244600-147249600	Weak transcription	NH-A	brain
18	chr4:147246200-147249600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:147246200-147254800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:147246200-147255000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:147246400-147254000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:147246800-147249800	Weak transcription	Liver	Liver
23	chr4:147247600-147255000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr4:147248800-147250200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:147248800-147252400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:147248800-147257200	Weak transcription	Fetal Intestine Large	intestine
27	chr4:147249000-147249800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:147249000-147249800	Enhancers	Lung	lung
29	chr4:147249000-147249800	Enhancers	Spleen	Spleen
30	chr4:147249000-147250800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:147249000-147252200	Enhancers	NHLF	lung
32	chr4:147249000-147252400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:147249000-147252400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:147249000-147252400	Enhancers	NHDF-Ad	bronchial
35	chr4:147249000-147252600	Enhancers	HMEC	breast
36	chr4:147249200-147249800	Enhancers	Esophagus	oesophagus
37	chr4:147249200-147251800	Enhancers	HSMM	muscle
38	chr4:147249200-147252200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:147249200-147252400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:147249200-147252400	Enhancers	Hela-S3	cervix
41	chr4:147249200-147252600	Enhancers	NHEK	skin
42	chr4:147249400-147250200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr4:147249400-147250200	Enhancers	HUVEC	blood vessel
44	chr4:147249400-147250400	Enhancers	HSMMtube	muscle
45	chr4:147249400-147251800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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