Variant report

Variant	rs10416812
Chromosome Location	chr19:20174057-20174058
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF90-2	chr19:20173564-20174129	NONHSAT063623

Extended variants
information (count: 100 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10404484	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10407270	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10408129	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10409512	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap]
rs10409614	0.96[ASN][1000 genomes]
rs10409629	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap]
rs10410313	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10420011	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap]
rs10420124	0.93[CEU][hapmap];0.95[CHB][hapmap]
rs10420900	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10423526	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10423976	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11085294	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11085295	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11085296	0.84[ASN][1000 genomes]
rs1121387	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1121388	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11668688	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11671950	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12463237	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975130	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976158	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12983056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12983683	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319479	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[EUR][1000 genomes]
rs17767339	0.90[ASN][1000 genomes]
rs1860939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1860940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1974650	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1974651	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017721	0.82[EUR][1000 genomes]
rs2159921	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215721	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286920	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2286921	0.93[CEU][hapmap];0.89[ASN][1000 genomes]
rs2286922	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2286923	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs2335888	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs2335889	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs2335892	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2335896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2335897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs258575	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs258579	0.81[CEU][hapmap]
rs4563152	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs5013556	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511066	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs6511069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511070	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511075	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71944124	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7246955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7247818	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs7248117	0.80[EUR][1000 genomes]
rs7248186	0.80[EUR][1000 genomes]
rs7250923	0.86[EUR][1000 genomes]
rs7256046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103855	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8104703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8104933	0.86[ASN][1000 genomes]
rs8106847	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap]
rs8107041	0.86[EUR][1000 genomes]
rs8112738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304964	0.83[EUR][1000 genomes]
rs9304965	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs963380	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
6	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
9	nsv870354	chr19:20043821-20576175	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
10	nsv1062018	chr19:20053658-20193556	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1066004	chr19:20053658-20592867	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
12	nsv543932	chr19:20053658-20592867	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
13	nsv1066564	chr19:20056348-20595412	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
14	nsv1066375	chr19:20061084-20574512	Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
15	nsv543934	chr19:20061084-20574512	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
16	esv3501977	chr19:20072180-20193556	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv3501978	chr19:20072180-20193556	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv1057309	chr19:20072886-20595412	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
19	nsv578801	chr19:20084681-20595412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
20	nsv1055694	chr19:20088866-20595412	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
21	nsv578802	chr19:20091702-20595412	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
22	nsv1064400	chr19:20101052-20595412	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
23	nsv911322	chr19:20111134-20193556	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1066045	chr19:20142912-20179084	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
26	nsv1066014	chr19:20165112-20595412	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
27	nsv1057107	chr19:20171392-20193556	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10416812	ZNF682	cis	lymphoblastoid	seeQTL
rs10416812	ZNF93	cis	cerebellum	SCAN
rs10416812	ZNF253	cis	Nerve Tibial	GTEx
rs10416812	ZNF682	cis	Muscle Skeletal	GTEx
rs10416812	ZNF253	cis	parietal	SCAN
rs10416812	ZNF682	cis	cerebellum	SCAN
rs10416812	SLC5A5	cis	parietal	SCAN
rs10416812	ZNF682	cis	parietal	SCAN
rs10416812	SAGE1	trans	parietal	SCAN
rs10416812	ZNF100	cis	cerebellum	SCAN
rs10416812	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs10416812	ATP13A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20170200-20178200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:20173400-20174200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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