Variant report

Variant	rs1676780
Chromosome Location	chr10:28617810-28617811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:28616149..28619065-chr10:28621804..28623481,2	K562	blood:
2	chr10:28590494..28592156-chr10:28616581..28618601,2	K562	blood:
3	chr10:28598132..28600794-chr10:28617282..28619368,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222374	Chromatin interaction
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1148176	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676781	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1762187	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776094	1.00[ASN][1000 genomes]
rs1776114	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776118	1.00[ASN][1000 genomes]
rs1776120	1.00[ASN][1000 genomes]
rs2797597	1.00[ASN][1000 genomes]
rs703020	1.00[ASN][1000 genomes]
rs703021	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs786393	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786396	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786691	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1044938	chr10:28601993-28659440	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28596800-28618800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr10:28614000-28619000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr10:28614800-28620600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:28615000-28620000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr10:28615200-28619200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr10:28615200-28621000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:28616000-28618200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr10:28616000-28619000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:28616000-28619600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:28616000-28621600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:28616200-28619200	Weak transcription	Fetal Thymus	thymus
12	chr10:28616200-28619800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr10:28616400-28618800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr10:28616400-28620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr10:28616600-28618800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:28616800-28618000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr10:28616800-28618200	Enhancers	Rectal Smooth Muscle	rectum
18	chr10:28616800-28618600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr10:28616800-28619000	Weak transcription	Primary B cells from cord blood	blood
20	chr10:28616800-28620600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr10:28616800-28623000	Weak transcription	Fetal Muscle Leg	muscle
22	chr10:28616800-28623800	Weak transcription	NHLF	lung
23	chr10:28617000-28618800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr10:28617000-28618800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr10:28617000-28618800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:28617000-28619000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr10:28617000-28619400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr10:28617000-28620600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:28617000-28621000	Enhancers	Colon Smooth Muscle	Colon
30	chr10:28617000-28621600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr10:28617000-28621600	Weak transcription	Pancreas	Pancrea
32	chr10:28617000-28622800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr10:28617200-28618200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr10:28617200-28621000	Weak transcription	NH-A	brain
35	chr10:28617400-28618000	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr10:28617400-28618000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr10:28617400-28618600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:28617400-28618800	Weak transcription	Primary T cells from cord blood	blood
39	chr10:28617400-28621000	Weak transcription	HMEC	breast
40	chr10:28617600-28618000	Weak transcription	HSMMtube	muscle
41	chr10:28617600-28621000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr10:28617600-28621000	Weak transcription	HSMM	muscle
43	chr10:28617800-28618800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:28617800-28621000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:28617800-28622600	Weak transcription	NHEK	skin
46	chr10:28617800-28623000	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links