Variant report

Variant	rs13108868
Chromosome Location	chr4:99083753-99083754
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	chr4:99083174..99085665-chr4:99180019..99182924,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138698	Chromatin interaction
ENSG00000214559	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10006414	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10032272	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097614	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11097615	0.84[EUR][1000 genomes]
rs11941885	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs13118892	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs13118945	0.84[CEU][hapmap]
rs13121558	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs13133619	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs13136721	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs13147921	0.90[CHB][hapmap]
rs13149968	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs1527516	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs1534319	0.87[CEU][hapmap]
rs17027308	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs17486413	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs1869351	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1921415	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28481322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2865986	0.86[CHB][hapmap]
rs2865988	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs2865990	0.90[CEU][hapmap]
rs28792413	0.84[EUR][1000 genomes]
rs2903152	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs3846446	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846447	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3857217	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs3896704	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs4345191	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs4443293	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs4577589	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4637413	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699324	0.84[CEU][hapmap]
rs4699332	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4699595	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs4699606	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699611	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532724	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs6814353	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6823718	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs6827474	0.84[EUR][1000 genomes]
rs6830176	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830245	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830594	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6839454	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs6852813	0.88[CEU][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854594	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs6854919	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs7377018	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs7656233	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs7663216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663438	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs7666738	0.85[CHB][hapmap]
rs7683769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684646	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs7687371	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7687958	0.87[CEU][hapmap];0.85[CHB][hapmap]
rs7691433	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs9994641	0.84[EUR][1000 genomes]
rs9998803	0.84[CEU][hapmap];0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002098	chr4:98501337-99086320	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv537193	chr4:98501337-99086320	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv879648	chr4:98547717-99104879	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1000011	chr4:98562308-99101692	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1000956	chr4:98732458-99178588	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv879650	chr4:99057457-99172232	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv998270	chr4:99063275-99120404	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv461595	chr4:99065480-99172175	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv594939	chr4:99065480-99172175	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv470061	chr4:99078105-99160699	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 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
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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