Variant report

Variant	rs13194254
Chromosome Location	chr6:106981439-106981440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11153004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153005	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153006	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11752138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11752150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13197493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13197786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353046	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2353048	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353049	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2883077	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6928187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6928541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1025510	chr6:106791080-106982400	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538404	chr6:106791080-106982400	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv15497	chr6:106981224-106982723	Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13194254	AIM1	cis	lymphoblastoid	seeQTL
rs13194254	AIM1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-106991000	Weak transcription	Spleen	Spleen
3	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
4	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:106973400-106985600	Weak transcription	Stomach Mucosa	stomach
6	chr6:106973600-106985800	Weak transcription	Thymus	Thymus
7	chr6:106973600-106986000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:106973600-106992800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:106974600-106982400	Strong transcription	Primary hematopoietic stem cells	blood
10	chr6:106974800-106982600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr6:106975000-106981600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:106975000-106983400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr6:106975200-106983000	Strong transcription	Adipose Nuclei	Adipose
14	chr6:106976000-106983200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr6:106976200-106982800	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:106976400-106981600	Strong transcription	Primary B cells from cord blood	blood
17	chr6:106976400-106986200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:106976600-106982000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:106976600-106991400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:106977000-106986400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:106977600-106981600	Genic enhancers	NHEK	skin
22	chr6:106978000-106982400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:106978600-106983400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:106978800-106981800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:106978800-106984200	Weak transcription	NH-A	brain
26	chr6:106978800-106985600	Weak transcription	Fetal Thymus	thymus
27	chr6:106978800-106993800	Weak transcription	NHLF	lung
28	chr6:106979000-106982200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
30	chr6:106979200-106982000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:106979400-106982200	Weak transcription	HUVEC	blood vessel
32	chr6:106979600-106984200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:106979600-106987200	Weak transcription	HepG2	liver
34	chr6:106980000-106982400	Strong transcription	Rectal Smooth Muscle	rectum
35	chr6:106980200-106983000	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr6:106980200-106984400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:106980400-106982800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr6:106980800-106981600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:106980800-106981800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:106980800-106981800	Genic enhancers	NHDF-Ad	bronchial
41	chr6:106980800-106982000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:106980800-106982200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr6:106980800-106982200	Strong transcription	Dnd41	blood
44	chr6:106980800-106982400	Enhancers	Placenta	Placenta
45	chr6:106980800-106982800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr6:106980800-106982800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr6:106980800-106982800	Genic enhancers	GM12878-XiMat	blood
48	chr6:106980800-106983200	Genic enhancers	Primary monocytes fromperipheralblood	blood
49	chr6:106980800-106983400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:106980800-106984400	Genic enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links