Variant report

Variant	rs28621675
Chromosome Location	chr4:1130436-1130437
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10002248	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10002437	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003030	0.86[AFR][1000 genomes]
rs10014245	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015944	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10016588	0.89[AFR][1000 genomes]
rs10027895	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029139	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11247974	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11726554	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11731643	0.87[AFR][1000 genomes]
rs11731685	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11732057	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11734374	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13435166	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1481167	0.98[AFR][1000 genomes]
rs17164384	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28540372	0.82[AFR][1000 genomes]
rs28578449	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28785628	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28855974	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28856334	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3775111	0.83[AFR][1000 genomes]
rs59465697	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6599282	0.98[AFR][1000 genomes]
rs6599283	0.98[AFR][1000 genomes]
rs6599284	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6599285	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6812059	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6831018	0.88[AFR][1000 genomes]
rs6836158	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6836335	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73065688	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73065696	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73065698	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73067706	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73067775	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73067776	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7661069	0.83[AFR][1000 genomes]
rs7669287	0.83[AFR][1000 genomes]
rs7676956	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7678661	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7679718	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7684536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685051	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7690300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7690832	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878324	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv1004727	chr4:1015652-1158207	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv536984	chr4:1015652-1158207	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1124800-1130800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr4:1124800-1131000	Weak transcription	GM12878-XiMat	blood
3	chr4:1124800-1149600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:1125200-1131000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:1127600-1131000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:1128400-1131200	Weak transcription	Hela-S3	cervix
7	chr4:1128800-1131000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:1128800-1131800	Enhancers	Thymus	Thymus
9	chr4:1129400-1131000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:1129600-1130600	Enhancers	Duodenum Mucosa	Duodenum
11	chr4:1129600-1131000	Enhancers	Primary B cells from peripheral blood	blood
12	chr4:1129600-1131000	Enhancers	Primary T cells from cord blood	blood
13	chr4:1129600-1131000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr4:1129600-1131000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:1129800-1130600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr4:1129800-1130800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:1129800-1131000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr4:1129800-1131000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr4:1129800-1131200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr4:1130000-1131000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr4:1130000-1131000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr4:1130200-1130600	Enhancers	Pancreas	Pancrea
23	chr4:1130200-1130800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr4:1130400-1130800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:1130400-1131000	Enhancers	Primary B cells from cord blood	blood
26	chr4:1130400-1131000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr4:1130400-1131200	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links