Variant report

Variant	rs6659798
Chromosome Location	chr1:152795971-152795972
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	CTCF	chr1:152795880-152796030	HMF	breast:	n/a	n/a
2	CTCF	chr1:152795877-152796095	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr1:152795920-152796070	GM12867	blood:	n/a	n/a
4	CTCF	chr1:152795880-152796030	GM12864	blood:	n/a	n/a
5	CTCF	chr1:152795900-152796050	GM12864	blood:	n/a	n/a
6	RAD21	chr1:152795781-152796138	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr1:152795840-152795990	GM12870	blood:	n/a	n/a
8	CTCF	chr1:152795920-152796070	GM12866	blood:	n/a	n/a
9	SMC3	chr1:152795815-152796147	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr1:152795880-152796030	HPF	lung:	n/a	n/a
11	CTCF	chr1:152795900-152796050	GM12868	blood:	n/a	n/a
12	CTCF	chr1:152795940-152796090	HPF	lung:	n/a	n/a
13	CTCF	chr1:152795880-152796030	GM12872	blood:	n/a	n/a
14	CTCF	chr1:152795940-152796090	GM12864	blood:	n/a	n/a
15	CTCF	chr1:152795860-152796010	GM12872	blood:	n/a	n/a
16	CTCF	chr1:152795880-152796030	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
LCE1A	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11205127	0.87[CHB][hapmap]
rs11205129	0.80[MEX][hapmap]
rs11804609	0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs12022319	0.82[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs12026193	0.91[CHB][hapmap]
rs12565568	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12568299	0.86[CHB][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap]
rs16834728	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs1819433	0.93[EUR][1000 genomes]
rs2339396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2339397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2339398	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs2339399	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3737861	0.80[CHD][hapmap]
rs4240862	0.90[CHB][hapmap]
rs4240863	0.91[CHB][hapmap]
rs4845325	0.82[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap]
rs4845492	0.81[MEX][hapmap]
rs7550676	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7552416	0.91[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
9	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1009885	chr1:152762750-152851273	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1010576	chr1:152791716-152827652	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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