Variant report

Variant	rs10853858
Chromosome Location	chr19:53716278-53716279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VN1R2-5	chr19:53716201-53719355	NONHSAT067648
2	lnc-VN1R2-5	chr19:53716241-53716649	NONHSAT147051

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10401578	0.92[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10425196	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775558	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853859	0.96[CEU][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084224	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11084225	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11084226	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11084227	0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1136205	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11666072	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11666631	0.80[ASN][1000 genomes]
rs11669455	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11670443	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11671568	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11671603	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11672812	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11672910	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879930	0.84[EUR][1000 genomes]
rs11879932	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462419	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12462452	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12462453	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12462484	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610332	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12972588	0.83[ASN][1000 genomes]
rs12982950	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12984188	0.89[CHD][hapmap]
rs12984473	0.83[CHD][hapmap]
rs12985503	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17206931	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17272903	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17272966	0.86[CHD][hapmap]
rs28734122	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2914372	0.83[CHD][hapmap]
rs2914383	0.86[CHD][hapmap]
rs2965242	0.81[CHD][hapmap]
rs34189836	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34535235	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35001955	0.87[EUR][1000 genomes]
rs35121915	0.81[EUR][1000 genomes]
rs35653121	0.83[EUR][1000 genomes]
rs36114232	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4358051	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4449055	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4801964	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801965	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801966	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4801968	0.88[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4801969	0.82[ASN][1000 genomes]
rs4801970	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803064	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803065	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803069	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59782712	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62117767	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62117782	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62117787	0.80[ASN][1000 genomes]
rs6509733	0.81[ASN][1000 genomes]
rs71363315	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7245395	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7245485	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7245880	0.83[EUR][1000 genomes]
rs7246839	0.82[EUR][1000 genomes]
rs7260577	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7260623	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription 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	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription 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	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10853858	ZNF818P	cis	lung	GTEx
rs10853858	ZNF154	cis	cerebellum	SCAN
rs10853858	ZNF587	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53701600-53720200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
2	chr19:53701600-53724800	ZNF genes & repeats	Liver	Liver
3	chr19:53701600-53725000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:53701600-53725000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:53701800-53718400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:53701800-53725400	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr19:53702400-53724800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:53706600-53716600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
9	chr19:53710600-53716800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:53711200-53716400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
11	chr19:53711200-53716600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:53711200-53717000	ZNF genes & repeats	Colon Smooth Muscle	Colon
13	chr19:53711200-53718000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:53711200-53720200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr19:53711400-53716400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
16	chr19:53711400-53716800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
17	chr19:53711400-53717000	ZNF genes & repeats	Primary B cells from cord blood	blood
18	chr19:53711600-53716800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
19	chr19:53711600-53716800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
20	chr19:53711600-53717000	ZNF genes & repeats	Brain Hippocampus Middle	brain
21	chr19:53711800-53716800	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
22	chr19:53711800-53716800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
23	chr19:53711800-53717000	ZNF genes & repeats	Brain Angular Gyrus	brain
24	chr19:53711800-53718000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:53712000-53717000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:53712200-53716800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:53712200-53718200	ZNF genes & repeats	Brain Substantia Nigra	brain
28	chr19:53712400-53716400	ZNF genes & repeats	Brain Germinal Matrix	brain
29	chr19:53712400-53717200	ZNF genes & repeats	Primary T cells from cord blood	blood
30	chr19:53712400-53717200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
31	chr19:53712400-53720200	ZNF genes & repeats	Brain Anterior Caudate	brain
32	chr19:53712600-53716600	ZNF genes & repeats	Fetal Lung	lung
33	chr19:53712600-53717000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:53712800-53716600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr19:53713800-53716800	ZNF genes & repeats	Psoas Muscle	Psoas
36	chr19:53715800-53716400	Active TSS	Fetal Heart	heart
37	chr19:53716000-53716800	ZNF genes & repeats	A549	lung

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