Variant report

Variant	rs1879497
Chromosome Location	chr19:37632877-37632878
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10403679	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10420554	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10424584	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1047333	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11084871	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11540540	0.86[EUR][1000 genomes]
rs11666897	0.82[EUR][1000 genomes]
rs11667146	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11670216	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11670374	0.83[EUR][1000 genomes]
rs11673192	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11673344	0.92[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12151313	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1234251	0.90[EUR][1000 genomes]
rs13345491	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1610560	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1644638	1.00[JPT][hapmap]
rs1644645	1.00[JPT][hapmap]
rs1657510	1.00[CHB][hapmap]
rs1667340	0.82[ASN][1000 genomes]
rs1667343	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16971873	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16971886	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16972020	1.00[CHB][hapmap]
rs16972024	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs16972028	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs16972030	1.00[CHB][hapmap]
rs17707446	0.88[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1962889	0.88[EUR][1000 genomes]
rs2011475	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562587	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745768	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3745770	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs45626541	0.90[EUR][1000 genomes]
rs496872	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs513406	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs540451	1.00[JPT][hapmap]
rs547483	0.92[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[ASN][1000 genomes]
rs55792845	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55856280	0.83[EUR][1000 genomes]
rs55921822	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56080874	0.81[EUR][1000 genomes]
rs56208574	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56210764	0.83[EUR][1000 genomes]
rs56330606	0.93[EUR][1000 genomes]
rs57916401	0.84[ASN][1000 genomes]
rs703530	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs703535	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs703537	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7247589	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252230	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7254616	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7256001	0.82[ASN][1000 genomes]
rs7256213	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7256746	0.92[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs7256876	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257126	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7257135	0.88[CEU][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7259513	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7260386	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs73622783	0.88[EUR][1000 genomes]
rs8104919	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106386	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107192	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8108727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110696	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826296	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs826303	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs826304	0.92[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs826322	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826323	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9676450	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription 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	73 gene(s)	inside rSNPs	diseases
6	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers 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	27 gene(s)	inside rSNPs	diseases
7	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
8	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
10	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS 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 target site	17 gene(s)	inside rSNPs	diseases
13	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv2477	chr19:37617348-37662207	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1879497	CEACAM16	cis	cerebellum	SCAN
rs1879497	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs1879497	HKR1	cis	lymphoblastoid	seeQTL
rs1879497	AC012309.5	cis	Thyroid	GTEx
rs1879497	AC012309.5	cis	Artery Tibial	GTEx
rs1879497	ARHGEF1	cis	cerebellum	SCAN
rs1879497	C19orf61	cis	cerebellum	SCAN
rs1879497	ZNF585B	cis	Artery Tibial	GTEx
rs1879497	B9D2	cis	parietal	SCAN
rs1879497	AC012309.5	cis	Heart Left Ventricle	GTEx
rs1879497	AC012309.5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37613400-37642200	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:37613400-37642200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:37613800-37662200	ZNF genes & repeats	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links