Variant report

Variant	rs2194316
Chromosome Location	chr16:72329510-72329511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72314956..72316572-chr16:72326957..72329841,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10153081	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12598914	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs16970800	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs16970850	0.80[AFR][1000 genomes]
rs1837020	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1946767	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2083030	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs28404857	0.82[ASN][1000 genomes]
rs6499568	0.83[ASN][1000 genomes]
rs7184674	0.98[ASN][1000 genomes]
rs7201904	0.97[ASN][1000 genomes]
rs8050066	0.80[ASN][1000 genomes]
rs8058851	0.96[ASN][1000 genomes]
rs806734	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs9889215	0.87[ASN][1000 genomes]
rs9921177	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9929435	0.92[ASN][1000 genomes]
rs9929470	1.00[ASN][1000 genomes]
rs9936793	0.80[AFR][1000 genomes]
rs9939039	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9940976	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats 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	58 gene(s)	inside rSNPs	diseases
4	nsv1059599	chr16:72219769-72342170	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2194316	PDPR	cis	parietal	SCAN
rs2194316	TERF2	cis	parietal	SCAN
rs2194316	CYB5B	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72302600-72332000	Weak transcription	Primary B cells from cord blood	blood
2	chr16:72315600-72353600	Weak transcription	Dnd41	blood
3	chr16:72316600-72334800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:72317400-72331800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr16:72325400-72342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:72326200-72334800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr16:72327200-72330000	Weak transcription	NHEK	skin
8	chr16:72327200-72332200	Weak transcription	Hela-S3	cervix
9	chr16:72329200-72329800	Enhancers	HepG2	liver
10	chr16:72329400-72329800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links