Variant report

Variant	rs713473
Chromosome Location	chr14:55904696-55904697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55904613..55905202-chr14:56806452..56807250,2	MCF-7	breast:
2	chr14:55894393..55896757-chr14:55902007..55905006,2	MCF-7	breast:
3	chr14:55904524..55905404-chr14:56941095..56941735,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10483641	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483646	1.00[CHD][hapmap]
rs17128484	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128488	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17672376	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs17672950	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs17673930	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs17675052	0.89[CEU][hapmap]
rs17740413	0.89[CEU][hapmap]
rs17741681	0.88[CEU][hapmap]
rs17741825	0.89[CEU][hapmap]
rs17742621	1.00[CHD][hapmap]
rs17743484	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17743595	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17744929	1.00[ASN][1000 genomes]
rs17745017	1.00[ASN][1000 genomes]
rs1959443	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984988	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41299189	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41437744	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45612333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59169706	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713474	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713475	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013528	0.81[CEU][hapmap]
rs8015252	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323280	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901959	chr14:55853724-55916225	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
3	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs713473	KTN1	cis	multi-tissue	Pritchard
rs713473	FBXO34	cis	parietal	SCAN
rs713473	FBXO34	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55897800-55907000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:55901600-55905200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr14:55901800-55905000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr14:55901800-55906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:55901800-55907000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr14:55901800-55907800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr14:55902600-55907000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr14:55903200-55904800	Enhancers	Fetal Intestine Small	intestine
9	chr14:55903800-55904800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr14:55904000-55904800	Weak transcription	HepG2	liver
11	chr14:55904000-55905000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:55904600-55904800	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links