Variant report

Variant	rs2215284
Chromosome Location	chr19:42175160-42175161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42168589..42171356-chr19:42173176..42175470,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1008577	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10403314	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10407280	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10422983	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425592	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12609443	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12609822	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12610950	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1548720	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1548721	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1548722	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1548723	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1548724	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1860329	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2109073	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2109074	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109075	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109076	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34596329	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3786868	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826894	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4416132	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60613767	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508990	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71334987	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7245419	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250319	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7251886	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8102488	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8104755	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104781	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113799	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063241	chr19:42057334-42175160	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv3422975	chr19:42106166-42212774	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2215284	KCNJ14	cis	parietal	SCAN
rs2215284	CEACAM4	cis	multi-tissue	Pritchard
rs2215284	CEACAM3	cis	multi-tissue	Pritchard
rs2215284	PVRL2	cis	parietal	SCAN
rs2215284	STRN4	cis	cerebellum	SCAN
rs2215284	SLC6A16	cis	parietal	SCAN
rs2215284	PSG3	cis	multi-tissue	Pritchard
rs2215284	PVR	cis	parietal	SCAN
rs2215284	NAPA	cis	parietal	SCAN
rs2215284	IL4I1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42174200-42175400	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr19:42174400-42175600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
3	chr19:42174800-42181800	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links