Variant report

Variant	rs8105629
Chromosome Location	chr19:21609556-21609557
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF708-1	chr19:21608886-21610284	ENSG00000196686

Extended variants
information (count: 119 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1012040	1.00[JPT][hapmap]
rs10406824	1.00[JPT][hapmap]
rs11085455	1.00[JPT][hapmap]
rs12150996	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12151067	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151068	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151222	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12971724	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12975330	0.83[ASN][1000 genomes]
rs12975981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12976011	0.83[ASN][1000 genomes]
rs12981869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12984238	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1500400	1.00[JPT][hapmap]
rs1500401	1.00[JPT][hapmap]
rs1520073	1.00[JPT][hapmap]
rs1533675	1.00[JPT][hapmap]
rs1566474	0.83[ASN][1000 genomes]
rs1566476	0.83[ASN][1000 genomes]
rs1566477	0.83[ASN][1000 genomes]
rs1607664	1.00[JPT][hapmap]
rs1678822	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs16997924	0.83[ASN][1000 genomes]
rs17618715	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17618778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17680671	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs1813234	0.86[CEU][hapmap]
rs1984771	1.00[JPT][hapmap]
rs2133816	1.00[JPT][hapmap]
rs2133820	1.00[JPT][hapmap]
rs2173724	1.00[JPT][hapmap]
rs2246914	1.00[JPT][hapmap]
rs2262897	0.83[ASN][1000 genomes]
rs2358984	0.87[CEU][hapmap]
rs2562399	1.00[JPT][hapmap]
rs2562448	1.00[JPT][hapmap]
rs2562457	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2562458	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2562459	0.83[ASN][1000 genomes]
rs2650778	0.83[ASN][1000 genomes]
rs2650779	1.00[JPT][hapmap]
rs2650780	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2650781	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2650782	0.83[ASN][1000 genomes]
rs2650783	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2650785	0.83[ASN][1000 genomes]
rs2650786	0.83[ASN][1000 genomes]
rs2650791	1.00[JPT][hapmap]
rs2650794	1.00[JPT][hapmap]
rs2650799	1.00[JPT][hapmap]
rs2650808	0.83[ASN][1000 genomes]
rs2650845	1.00[CEU][hapmap]
rs2681371	1.00[JPT][hapmap]
rs2681372	1.00[JPT][hapmap]
rs28839521	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2914636	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2914647	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2937161	0.80[EUR][1000 genomes]
rs2968081	0.83[ASN][1000 genomes]
rs34560125	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34875588	0.88[EUR][1000 genomes]
rs35148123	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35245030	0.83[ASN][1000 genomes]
rs35578515	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35860067	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4332859	0.83[ASN][1000 genomes]
rs4341872	1.00[CEU][hapmap]
rs488125	0.86[CEU][hapmap]
rs501647	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs504280	0.82[CEU][hapmap]
rs509540	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs56152627	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs566230	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs57841525	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110379	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62111469	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62111470	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62111476	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629548	1.00[JPT][hapmap]
rs6511247	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs669046	1.00[JPT][hapmap]
rs67723811	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs685844	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7246684	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7249636	0.86[CEU][hapmap]
rs7254436	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs7254762	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs7257584	0.83[ASN][1000 genomes]
rs7258211	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7258523	0.80[ASN][1000 genomes]
rs7259178	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8100318	1.00[JPT][hapmap]
rs8101077	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8101442	0.83[ASN][1000 genomes]
rs8102655	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8102854	1.00[JPT][hapmap]
rs8103151	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8105404	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8107042	0.84[EUR][1000 genomes]
rs8107940	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8107999	1.00[CHB][hapmap];0.80[YRI][hapmap]
rs8111189	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs8112359	0.80[ASN][1000 genomes]
rs8113558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak 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	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8105629	ZNF738	cis	Thyroid	GTEx
rs8105629	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs8105629	ZNF429	cis	Artery Aorta	GTEx
rs8105629	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs8105629	ZNF738	cis	Adipose Subcutaneous	GTEx
rs8105629	ZNF429	cis	Whole Blood	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
3	chr19:21599600-21611000	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:21600000-21613000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:21604400-21610400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr19:21605600-21610800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:21605600-21610800	Weak transcription	Ovary	ovary
8	chr19:21607600-21630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:21609000-21610000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links