Variant report

Variant	rs6671066
Chromosome Location	chr1:75103028-75103029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr1:75102867-75103041	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75100938..75103677-chr20:57465858..57468191,2	MCF-7	breast:

Variant related genes	Relation type
C1orf173	TF binding region
ENSG00000087460	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10493546	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10789399	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap]
rs10890136	0.81[GIH][hapmap]
rs10890137	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs10890138	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11210488	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11210489	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11210490	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11210492	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12096336	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12117493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12123598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127070	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12137637	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239912	0.80[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs1340987	0.89[CEU][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1378278	0.98[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs1424667	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563291	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1834189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3845355	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs4650002	0.89[CEU][hapmap]
rs6660278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6701034	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs9326117	0.88[CEU][hapmap]
rs9661462	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv830248	chr1:74962391-75144458	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv870824	chr1:75019390-75125581	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv871239	chr1:75057586-75125581	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75102800-75103200	Enhancers	H1 Cell Line	embryonic stem cell
2	chr1:75102800-75103200	Enhancers	H9 Cell Line	embryonic stem cell
3	chr1:75102800-75103200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:75102800-75103200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:75102800-75103200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr1:75102800-75103200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:75102800-75103400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:75102800-75103400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:75103000-75103600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:75103000-75103600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:75103000-75103800	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links