Variant report

Variant	rs12708436
Chromosome Location	chr15:54897474-54897475
allele	A/C/G
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	chr15:54897174-54897544	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:54896939-54898132	GM12878	blood:	n/a	n/a
3	RAD21	chr15:54897201-54897478	H1-hESC	embryonic stem cell:	n/a	chr15:54897373-54897383

Variant related genes	Relation type
UNC13C	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10220855	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11632253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632366	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11852668	0.82[ASN][1000 genomes]
rs11852743	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs11856235	0.86[JPT][hapmap]
rs12592900	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12592914	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1356857	0.80[EUR][1000 genomes]
rs1520411	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs1818704	0.92[CEU][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1818711	0.88[CEU][hapmap];0.80[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1850994	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1851000	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1851005	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1851010	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1972137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414327	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2414331	0.88[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2414332	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2460605	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460606	0.96[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2460608	0.82[EUR][1000 genomes]
rs2553216	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2553217	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2553220	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553221	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553225	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2681958	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2681959	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2681964	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681965	0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681966	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2911846	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2911847	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2947001	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2947003	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3848141	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3959676	0.84[CEU][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493694	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493695	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174529	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9284299	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv904236	chr15:54820897-54912439	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1039548	chr15:54856965-54914519	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv569508	chr15:54876212-54904782	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv526413	chr15:54876423-54904782	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv904237	chr15:54888537-54927484	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv569509	chr15:54888537-54932716	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv457154	chr15:54892583-54904782	Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv569517	chr15:54892583-54904782	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54896000-54898600	Enhancers	Fetal Lung	lung
2	chr15:54896600-54897800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr15:54896600-54898000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr15:54896800-54897600	Enhancers	Fetal Intestine Large	intestine
5	chr15:54896800-54897800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:54896800-54898400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:54896800-54899800	Weak transcription	Aorta	Aorta
8	chr15:54897000-54897800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr15:54897000-54897800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:54897000-54898000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr15:54897200-54898200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr15:54897400-54897800	Enhancers	Fetal Stomach	stomach

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