Variant report

Variant	rs12592326
Chromosome Location	chr15:58554042-58554043
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	chr15:58554022-58554056	Lung_OC	lung:	n/a	n/a
2	STAT1	chr15:58552315-58554192	Hela-S3	cervix:	n/a	chr15:58552678-58552686 chr15:58552623-58552632 chr15:58553376-58553384 chr15:58552621-58552632 chr15:58552622-58552631

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58553979..58557970-chr15:58560575..58563562,3	K562	blood:

Variant related genes	Relation type
ALDH1A2	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12904030	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs1663260	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17240685	0.82[CEU][hapmap];0.87[AMR][1000 genomes]
rs1814867	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2414561	0.82[CEU][hapmap];0.89[AMR][1000 genomes]
rs2414563	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34149555	0.89[AMR][1000 genomes]
rs34458264	0.87[AMR][1000 genomes]
rs35348919	0.87[AMR][1000 genomes]
rs35779246	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36045724	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4542601	0.80[AMR][1000 genomes]
rs62000520	0.87[AMR][1000 genomes]
rs7164378	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173510	0.88[AMR][1000 genomes]
rs7178320	0.82[CEU][hapmap];0.85[AMR][1000 genomes]
rs7178332	0.85[AMR][1000 genomes]
rs7178337	0.85[AMR][1000 genomes]
rs7178779	0.82[CEU][hapmap];0.85[AMR][1000 genomes]
rs7179597	0.85[AMR][1000 genomes]
rs7179609	0.81[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7179726	0.89[AMR][1000 genomes]
rs7181607	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7183294	0.82[YRI][hapmap]
rs7184031	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72739137	0.91[ASN][1000 genomes]
rs8033046	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8040159	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8042351	0.83[AMR][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	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv833024	chr15:58447459-58621963	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1050473	chr15:58479888-58562270	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv904264	chr15:58505122-58588510	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv904265	chr15:58517528-58588510	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58547800-58557000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:58549600-58558600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:58550400-58561800	Weak transcription	Liver	Liver
4	chr15:58551800-58554400	Enhancers	Placenta	Placenta
5	chr15:58552400-58554200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:58552400-58554400	Enhancers	Psoas Muscle	Psoas
7	chr15:58552800-58554200	Enhancers	Left Ventricle	heart
8	chr15:58553200-58555000	Weak transcription	K562	blood
9	chr15:58553200-58562200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:58553400-58555600	Weak transcription	Primary T cells from cord blood	blood
11	chr15:58553400-58557000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:58553400-58562400	Weak transcription	Spleen	Spleen
13	chr15:58553600-58556600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:58553600-58559000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:58553600-58559000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:58553800-58554200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:58553800-58557200	Enhancers	Right Atrium	heart
18	chr15:58553800-58557200	Enhancers	Hela-S3	cervix
19	chr15:58554000-58554200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr15:58554000-58555000	Weak transcription	Right Ventricle	heart
21	chr15:58554000-58556200	Weak transcription	NHEK	skin
22	chr15:58554000-58556800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:58554000-58559200	Weak transcription	HMEC	breast

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