Variant report

Variant	rs2899609
Chromosome Location	chr15:58259597-58259598
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	POLR2A	chr15:58255933-58266423	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58258528..58260407-chr15:58261970..58264281,2	K562	blood:
2	chr15:58253084..58256788-chr15:58257302..58261139,5	K562	blood:

Variant related genes	Relation type
ALDH1A2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10518955	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11071358	0.86[EUR][1000 genomes]
rs11071359	1.00[EUR][1000 genomes]
rs11071360	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11635954	1.00[EUR][1000 genomes]
rs12595564	1.00[EUR][1000 genomes]
rs12903093	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12910509	1.00[EUR][1000 genomes]
rs1441816	1.00[EUR][1000 genomes]
rs1441817	0.86[EUR][1000 genomes]
rs1822206	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1837852	0.97[EUR][1000 genomes]
rs1837853	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1837855	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1899354	1.00[EUR][1000 genomes]
rs1964429	0.86[EUR][1000 genomes]
rs2012147	0.86[EUR][1000 genomes]
rs2165572	0.97[EUR][1000 genomes]
rs2197093	1.00[EUR][1000 genomes]
rs2218261	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2642616	0.94[EUR][1000 genomes]
rs2704195	0.85[EUR][1000 genomes]
rs2704219	0.94[EUR][1000 genomes]
rs2704220	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34907369	0.81[EUR][1000 genomes]
rs35343865	0.81[EUR][1000 genomes]
rs35648920	0.97[EUR][1000 genomes]
rs36018359	0.97[EUR][1000 genomes]
rs36071236	0.97[EUR][1000 genomes]
rs4775008	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493972	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493973	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176918	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8028082	1.00[EUR][1000 genomes]
rs8041922	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9635347	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9635348	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9635349	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833023	chr15:58161839-58340174	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv569593	chr15:58201698-58308650	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv904256	chr15:58253269-58274229	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv904257	chr15:58253894-58281035	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv904258	chr15:58255305-58281035	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv904259	chr15:58256296-58274229	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv904260	chr15:58257123-58276747	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv904261	chr15:58258424-58347260	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58248800-58262400	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:58253800-58271600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:58253800-58284800	Weak transcription	Ovary	ovary
4	chr15:58254400-58260000	Weak transcription	Left Ventricle	heart
5	chr15:58254400-58260000	Weak transcription	Right Atrium	heart
6	chr15:58258000-58260000	Weak transcription	Fetal Kidney	kidney
7	chr15:58258000-58272200	Weak transcription	Right Ventricle	heart
8	chr15:58259000-58264600	Weak transcription	Fetal Lung	lung
9	chr15:58259200-58261200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links