Variant report

Variant	rs9902683
Chromosome Location	chr17:20015428-20015429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC144C-3	chr17:20015137-20016303	NONHSAT146542

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

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

rs_ID	r²[population]
rs11868429	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs12051550	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12051865	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs13339684	0.88[EUR][1000 genomes]
rs16942325	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16959946	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16960660	0.89[EUR][1000 genomes]
rs16960678	0.89[EUR][1000 genomes]
rs16960700	0.94[ASN][1000 genomes]
rs16960717	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[AMR][1000 genomes]
rs16960730	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs16964352	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1971043	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[ASN][1000 genomes]
rs1971044	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28550747	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28567541	0.89[EUR][1000 genomes]
rs28622601	0.89[EUR][1000 genomes]
rs28644386	0.88[EUR][1000 genomes]
rs3751979	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs3764436	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025290	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56138907	0.89[EUR][1000 genomes]
rs61141789	0.94[ASN][1000 genomes]
rs6587061	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs6587218	0.98[ASN][1000 genomes]
rs7210439	0.89[EUR][1000 genomes]
rs7213349	1.00[ASN][1000 genomes]
rs7213816	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7215097	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7215432	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7225605	0.89[EUR][1000 genomes]
rs73299658	0.94[ASN][1000 genomes]
rs73301548	0.81[ASN][1000 genomes]
rs73981803	0.94[EUR][1000 genomes]
rs73981807	0.94[EUR][1000 genomes]
rs73981849	0.82[AMR][1000 genomes]
rs73984564	0.88[EUR][1000 genomes]
rs73984568	0.88[EUR][1000 genomes]
rs73984571	0.89[EUR][1000 genomes]
rs73984573	0.89[EUR][1000 genomes]
rs8077051	0.94[ASN][1000 genomes]
rs9889684	0.94[EUR][1000 genomes]
rs9895177	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9897161	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9897168	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9899514	1.00[CHB][hapmap];0.86[AMR][1000 genomes]
rs9901357	0.96[EUR][1000 genomes]
rs9901484	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9908032	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9908418	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9909156	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9911605	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9911879	0.94[EUR][1000 genomes]
rs9913018	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9916729	0.89[EUR][1000 genomes]
rs9941362	1.00[CHB][hapmap]
rs9941376	1.00[CHB][hapmap]

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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases
11	nsv960437	chr17:20015227-20018343	Weak transcription Enhancers Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9902683	AKAP10	cis	Whole Blood	GTEx
rs9902683	USP32P3	cis	Nerve Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr17:20002200-20018800	Weak transcription	Spleen	Spleen
3	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:20007400-20024200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:20007600-20019800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr17:20007600-20020200	Weak transcription	Brain Angular Gyrus	brain
7	chr17:20007600-20024000	Weak transcription	Brain Substantia Nigra	brain
8	chr17:20007800-20017800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:20007800-20020200	Weak transcription	Brain Anterior Caudate	brain
10	chr17:20007800-20024000	Weak transcription	Brain Hippocampus Middle	brain
11	chr17:20009200-20024200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:20010800-20017200	Weak transcription	Primary T cells from cord blood	blood
13	chr17:20011800-20019200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr17:20012000-20018400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr17:20012600-20019800	Weak transcription	A549	lung
16	chr17:20013400-20016000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:20013600-20016400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:20014400-20019800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr17:20014400-20020000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:20014400-20024200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:20014400-20024400	Weak transcription	Ovary	ovary
22	chr17:20014400-20024800	Weak transcription	Aorta	Aorta
23	chr17:20014400-20025200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:20014600-20028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:20015000-20016400	Strong transcription	Adipose Nuclei	Adipose
26	chr17:20015200-20016200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:20015200-20017800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links