Variant report

Variant	rs2893820
Chromosome Location	chr6:26295686-26295687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26295031..26297314-chr6:26320254..26322863,2	MCF-7	breast:
2	chr6:26295280..26297298-chr6:26298881..26301425,2	MCF-7	breast:
3	chr6:26295127..26298066-chr6:26310919..26313160,2	MCF-7	breast:
4	chr6:26293428..26296289-chr6:26305462..26307059,2	MCF-7	breast:
5	chr6:7225243..7228202-chr6:26294425..26296298,2	K562	blood:
6	chr6:26294336..26297863-chr6:27099343..27102904,4	K562	blood:
7	chr6:26295370..26298315-chr6:27861809..27863582,2	K562	blood:
8	chr6:26295061..26296606-chr6:26303262..26305423,2	MCF-7	breast:
9	chr6:26295520..26298937-chr6:26299189..26303889,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124635	Chromatin interaction
ENSG00000220875	Chromatin interaction
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1053860	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10946810	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11751978	0.83[JPT][hapmap]
rs11752014	0.83[JPT][hapmap]
rs12525187	0.81[EUR][1000 genomes]
rs12660432	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12661552	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665035	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13210340	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16891523	0.83[JPT][hapmap]
rs16891525	0.83[JPT][hapmap]
rs17608582	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1883213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883214	0.83[JPT][hapmap]
rs1987244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393649	0.90[EUR][1000 genomes]
rs2893842	0.87[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs2893843	0.92[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs3778279	0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4412193	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs4631273	0.83[JPT][hapmap]
rs56763414	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61324092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61534839	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62394764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62394768	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62394769	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6456713	0.84[ASN][1000 genomes]
rs6914596	0.83[JPT][hapmap]
rs6918325	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6930616	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs6932584	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6932727	0.84[ASN][1000 genomes]
rs6933139	0.84[ASN][1000 genomes]
rs725575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755741	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs9357005	0.81[EUR][1000 genomes]
rs9358914	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9358916	0.82[EUR][1000 genomes]
rs9358918	0.88[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9358920	0.83[EUR][1000 genomes]
rs9358924	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9358925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9358926	0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9358927	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs9366648	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366650	0.81[EUR][1000 genomes]
rs9379842	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379844	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379845	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393691	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs9393696	0.83[EUR][1000 genomes]
rs9393697	0.83[EUR][1000 genomes]
rs9393700	0.88[ASN][1000 genomes]
rs989133	0.91[EUR][1000 genomes]
rs994379	0.88[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
7	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
8	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
9	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
10	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription 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	184 gene(s)	inside rSNPs	diseases
11	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2893820	IL32	trans	lymphoblastoid	seeQTL
rs2893820	ACOT13	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26293800-26296400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:26294400-26296800	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr6:26294600-26295800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:26294600-26295800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr6:26294600-26299200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:26294800-26295800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:26294800-26299200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:26295000-26298800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:26295400-26295800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:26295400-26295800	Enhancers	HMEC	breast
11	chr6:26295400-26295800	Enhancers	NHEK	skin
12	chr6:26295400-26297600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:26295400-26297600	Enhancers	Fetal Muscle Leg	muscle
14	chr6:26295600-26295800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:26295600-26295800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:26295600-26295800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:26295600-26295800	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr6:26295600-26295800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:26295600-26295800	Enhancers	A549	lung
20	chr6:26295600-26295800	Flanking Active TSS	HepG2	liver
21	chr6:26295600-26295800	Enhancers	HSMMtube	muscle
22	chr6:26295600-26295800	Enhancers	NH-A	brain
23	chr6:26295600-26296000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:26295600-26296000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:26295600-26296000	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr6:26295600-26296000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:26295600-26296000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr6:26295600-26296200	Enhancers	Primary B cells from peripheral blood	blood
29	chr6:26295600-26296200	Flanking Active TSS	Fetal Intestine Large	intestine
30	chr6:26295600-26296200	Active TSS	Psoas Muscle	Psoas
31	chr6:26295600-26296200	Flanking Active TSS	GM12878-XiMat	blood
32	chr6:26295600-26296400	Flanking Active TSS	Fetal Intestine Small	intestine
33	chr6:26295600-26296400	Flanking Active TSS	Osteobl	bone
34	chr6:26295600-26296600	Flanking Active TSS	Hela-S3	cervix
35	chr6:26295600-26296800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:26295600-26296800	Enhancers	Dnd41	blood
37	chr6:26295600-26297000	Enhancers	Stomach Mucosa	stomach
38	chr6:26295600-26297000	Transcr. at gene 5' and 3'	K562	blood
39	chr6:26295600-26297400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:26295600-26297400	Enhancers	Placenta	Placenta
41	chr6:26295600-26297600	Enhancers	HUVEC	blood vessel
42	chr6:26295600-26298000	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links