Variant report

Variant	rs740517
Chromosome Location	chr17:67083139-67083140
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1011789	0.84[TSI][hapmap]
rs1024598	0.84[TSI][hapmap]
rs11077403	0.84[TSI][hapmap]
rs11077942	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654867	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11657954	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11659091	0.89[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs12453921	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12942011	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12942993	0.98[ASN][1000 genomes]
rs1974575	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2098034	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302132	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302133	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302134	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2302290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2364315	0.87[CEU][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2364991	0.82[TSI][hapmap]
rs2364992	0.84[TSI][hapmap]
rs4603621	0.82[TSI][hapmap]
rs4968833	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968838	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs4968839	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs4968995	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213831	0.81[GIH][hapmap]
rs763920	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064583	0.84[TSI][hapmap]
rs8064595	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs8071373	0.84[TSI][hapmap]
rs8077252	0.82[TSI][hapmap]
rs8079981	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs8080693	0.84[TSI][hapmap]
rs9282552	0.92[EUR][1000 genomes]
rs981453	0.84[TSI][hapmap]
rs9909216	0.82[TSI][hapmap]
rs9914684	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1066998	chr17:67060038-67090475	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv908705	chr17:67061898-67112456	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	esv1850212	chr17:67081732-67117428	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs740517	ABCA9	cis	parietal	SCAN
rs740517	CACNG5	cis	cerebellum	SCAN
rs740517	ABCA6	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67065600-67088600	Weak transcription	Pancreas	Pancrea
2	chr17:67067200-67099600	Weak transcription	Gastric	stomach
3	chr17:67067200-67111600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr17:67071800-67091400	Weak transcription	Brain Anterior Caudate	brain
5	chr17:67074600-67083800	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr17:67075600-67085600	Strong transcription	Fetal Lung	lung
7	chr17:67076800-67109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr17:67077800-67137800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:67079400-67084200	Strong transcription	Adipose Nuclei	Adipose
10	chr17:67079400-67087400	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:67079400-67090600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr17:67079400-67093600	Weak transcription	Fetal Stomach	stomach
13	chr17:67079400-67095600	Weak transcription	Psoas Muscle	Psoas
14	chr17:67079400-67112200	Strong transcription	Liver	Liver
15	chr17:67079400-67112600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:67079400-67117600	Weak transcription	Esophagus	oesophagus
17	chr17:67079600-67091600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr17:67079600-67101200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:67079600-67114200	Weak transcription	NHDF-Ad	bronchial
20	chr17:67080000-67085000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:67080600-67083600	Weak transcription	Lung	lung
22	chr17:67080600-67086600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:67080800-67088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr17:67080800-67088600	Weak transcription	GM12878-XiMat	blood
25	chr17:67080800-67090800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr17:67080800-67112000	Weak transcription	Brain Substantia Nigra	brain
27	chr17:67081200-67086200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:67081200-67088200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:67081200-67088600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr17:67081200-67090800	Weak transcription	Fetal Muscle Leg	muscle
31	chr17:67081200-67102000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr17:67081400-67089400	Weak transcription	Ovary	ovary
33	chr17:67081400-67090400	Weak transcription	Left Ventricle	heart
34	chr17:67081400-67095000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr17:67081400-67118600	Weak transcription	Right Ventricle	heart
36	chr17:67082200-67114400	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links