Variant report

Variant	rs429951
Chromosome Location	chr19:20999614-20999615
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF85-2	chr19:20997935-21000305	ENSG00000250870

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10404578	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10409571	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10410434	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10411595	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10413212	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10413434	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10419799	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10424164	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10425212	0.83[EUR][1000 genomes]
rs11085399	0.84[ASN][1000 genomes]
rs11085400	0.84[ASN][1000 genomes]
rs11085401	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11668918	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12463381	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12608830	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12973017	0.82[ASN][1000 genomes]
rs12974289	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976813	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12979116	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12981973	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1974808	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2059140	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2081887	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2081888	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2081891	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2099048	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2115091	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2115098	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2161462	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2162792	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2358609	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2545173	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2545221	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2545229	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547127	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547161	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2547162	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2547173	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2547174	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2547181	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2560963	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs364293	0.85[AFR][1000 genomes]
rs366654	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs399686	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4263059	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs431157	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs439388	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs448677	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4809117	0.84[ASN][1000 genomes]
rs4809118	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs622661	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625998	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs645200	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6511157	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6511158	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6511160	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7246681	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250207	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7251516	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7254049	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7254973	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7256021	0.86[AFR][1000 genomes]
rs7256449	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7257140	0.84[ASN][1000 genomes]
rs7257229	0.86[AFR][1000 genomes]
rs7258122	0.84[ASN][1000 genomes]
rs7259374	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7259970	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7507539	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8100852	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8100986	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8102151	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8113412	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9304976	0.83[AMR][1000 genomes]
rs9676612	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv530804	chr19:20574295-21001349	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
3	nsv578918	chr19:20818886-21008212	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic 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	12 gene(s)	inside rSNPs	diseases
4	esv3447275	chr19:20818886-21030779	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking 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	13 gene(s)	inside rSNPs	diseases
5	esv2752729	chr19:20818886-21169554	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic 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 target site	19 gene(s)	inside rSNPs	diseases
6	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv578934	chr19:20845947-21001176	Active TSS ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS 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
10	nsv911409	chr19:20845947-21001176	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv3338155	chr19:20845947-21015656	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	esv3319109	chr19:20845947-21015695	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv3319110	chr19:20845947-21015695	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Genic 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	11 gene(s)	inside rSNPs	diseases
14	nsv1056154	chr19:20845947-21021053	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking 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	11 gene(s)	inside rSNPs	diseases
15	nsv543940	chr19:20845947-21021053	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers 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	11 gene(s)	inside rSNPs	diseases
16	nsv1067170	chr19:20845947-21041038	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers 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	12 gene(s)	inside rSNPs	diseases
17	nsv458512	chr19:20845947-21041350	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv578926	chr19:20845947-21041350	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv578935	chr19:20845947-21048883	Strong transcription ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv578936	chr19:20845947-21049204	Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv1064103	chr19:20845947-21062996	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv432036	chr19:20851860-21001960	ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv578942	chr19:20899284-21049204	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv911410	chr19:20908079-21001176	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	nsv1067085	chr19:20912304-21008838	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
26	nsv1067001	chr19:20926564-21002094	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
27	nsv1064657	chr19:20926564-21008838	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
28	nsv1063751	chr19:20928739-21007706	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
29	nsv578944	chr19:20946275-21048883	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
30	nsv978787	chr19:20959523-21002686	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
31	nsv578945	chr19:20980958-21041350	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs429951	ZNF85	Cis_1M	lymphoblastoid	RTeQTL
rs429951	ZNF85	cis	Stomach	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20990800-21001200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:20991000-21006800	Weak transcription	Ovary	ovary
3	chr19:20996800-21000400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:20999000-21006600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:20999400-21001800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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