Variant report

Variant	rs279813
Chromosome Location	chr19:21468316-21468317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF738-5	chr19:21467908-21468489	ucscGeneNc_uc002nqb_2

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1055753	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11085441	0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11085443	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11085447	0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs11667770	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs12610331	0.80[ASN][1000 genomes]
rs12975081	0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap]
rs12975981	0.86[CEU][hapmap]
rs12981564	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap]
rs12981735	0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap]
rs12981869	0.86[CEU][hapmap]
rs12982282	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs12984300	0.80[ASN][1000 genomes]
rs1678822	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17618778	0.87[CEU][hapmap]
rs1762580	0.81[EUR][1000 genomes]
rs1781863	0.89[EUR][1000 genomes]
rs1781873	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1813234	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2012013	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs2086319	0.81[JPT][hapmap]
rs2088762	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs2170024	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2358984	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2650798	0.81[JPT][hapmap]
rs2650845	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs279797	0.80[JPT][hapmap];0.92[YRI][hapmap]
rs28688205	0.89[ASN][1000 genomes]
rs2914636	1.00[CEU][hapmap]
rs2914638	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2914645	0.80[JPT][hapmap]
rs2928208	0.83[EUR][1000 genomes]
rs2937174	0.81[JPT][hapmap]
rs2968045	0.81[JPT][hapmap]
rs4315457	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs4341872	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs4621113	0.89[CHB][hapmap]
rs483383	0.80[EUR][1000 genomes]
rs488125	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs501647	1.00[CEU][hapmap]
rs504280	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs509540	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs531283	0.82[EUR][1000 genomes]
rs565406	0.82[EUR][1000 genomes]
rs566230	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs617186	0.81[EUR][1000 genomes]
rs629548	0.90[CEU][hapmap]
rs6511222	0.80[ASN][1000 genomes]
rs6511228	0.86[EUR][1000 genomes]
rs6511239	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs669046	0.91[CEU][hapmap]
rs685844	1.00[CEU][hapmap]
rs7247411	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs7248601	0.89[JPT][hapmap]
rs7249412	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7249636	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7252261	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs7252873	0.86[EUR][1000 genomes]
rs7257857	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7258086	0.86[EUR][1000 genomes]
rs7259311	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7508671	0.88[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs8099940	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap]
rs8102328	0.86[EUR][1000 genomes]
rs8103325	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs8103459	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs8105629	0.87[CEU][hapmap]
rs8110470	0.80[EUR][1000 genomes]
rs8110967	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs8111189	1.00[CEU][hapmap]
rs8113558	0.87[CEU][hapmap]
rs924485	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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
2	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
3	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
4	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
5	nsv578950	chr19:21388995-21477431	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	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
11	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
12	esv2762027	chr19:21465718-21474111	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs279813	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs279813	ZNF493	cis	Lymphoblastoid	GTEx
rs279813	ZNF429	cis	Adipose Subcutaneous	GTEx
rs279813	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs279813	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs279813	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs279813	CTD-2561J22.5	cis	Thyroid	GTEx
rs279813	ZNF493	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21465400-21484600	ZNF genes & repeats	Liver	Liver
3	chr19:21467000-21472800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:21467200-21470000	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr19:21467200-21489600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:21468000-21474200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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