Variant report

Variant	rs6799809
Chromosome Location	chr3:146263575-146263576
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146254115..146256698-chr3:146261297..146263941,3	MCF-7	breast:
2	chr3:146234146..146236591-chr3:146261590..146264248,2	K562	blood:

Variant related genes	Relation type
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1061307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1079369	0.89[CHB][hapmap]
rs13064509	0.89[CHB][hapmap];0.89[YRI][hapmap]
rs13069082	0.89[CHB][hapmap]
rs13080178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997601	0.88[CHB][hapmap]
rs34009190	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34598718	0.85[ASN][1000 genomes]
rs35766154	0.94[ASN][1000 genomes]
rs3773521	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs60601385	0.85[ASN][1000 genomes]
rs66639703	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7625626	0.88[CEU][hapmap];0.84[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647634	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815834	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861142	0.89[CHB][hapmap]
rs9876886	0.89[CHB][hapmap]
rs9880682	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9883058	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146261400-146263800	Active TSS	NHLF	lung
2	chr3:146262800-146263600	Enhancers	HepG2	liver
3	chr3:146262800-146264000	Weak transcription	Brain Substantia Nigra	brain
4	chr3:146262800-146267600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:146262800-146268600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:146263000-146263600	Enhancers	Duodenum Mucosa	Duodenum
7	chr3:146263000-146263800	Weak transcription	GM12878-XiMat	blood
8	chr3:146263000-146264000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:146263000-146264600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:146263000-146267800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:146263200-146263600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:146263200-146263600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:146263200-146263600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:146263200-146263600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:146263200-146263600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:146263200-146263800	Enhancers	K562	blood
17	chr3:146263200-146264000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:146263200-146265600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:146263200-146265600	Enhancers	HMEC	breast
20	chr3:146263200-146267000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:146263200-146267000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:146263200-146267200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:146263200-146267400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:146263200-146267400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:146263200-146267400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:146263200-146267400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:146263200-146267600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:146263200-146267600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:146263200-146267600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:146263200-146267600	Weak transcription	Liver	Liver
31	chr3:146263200-146267800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:146263200-146268000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:146263200-146268000	Weak transcription	Osteobl	bone
34	chr3:146263200-146268200	Weak transcription	A549	lung
35	chr3:146263200-146268800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:146263200-146268800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:146263200-146270800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:146263400-146263800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:146263400-146264400	Weak transcription	Hela-S3	cervix
40	chr3:146263400-146265000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:146263400-146265200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:146263400-146265200	Enhancers	NHEK	skin
43	chr3:146263400-146267400	Weak transcription	Dnd41	blood
44	chr3:146263400-146267600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:146263400-146267600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:146263400-146267600	Weak transcription	Primary B cells from cord blood	blood
47	chr3:146263400-146267600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:146263400-146267600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:146263400-146267800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:146263400-146267800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links