Variant report

Variant	rs12594642
Chromosome Location	chr15:55994358-55994359
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	chr15:55993287..55995183-chr15:55997078..55999986,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1014551	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10518817	0.80[CEU][hapmap];0.88[AMR][1000 genomes]
rs10851589	0.80[CEU][hapmap]
rs11857453	0.85[ASN][1000 genomes]
rs11857467	0.86[ASN][1000 genomes]
rs11858195	0.83[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12373006	0.87[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap]
rs12591246	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12592192	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1371056	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1530087	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1550330	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16976450	0.90[MEX][hapmap];0.84[AMR][1000 genomes]
rs16976466	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs16976472	0.82[JPT][hapmap]
rs1986012	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2414424	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414426	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414427	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs572531	0.95[MEX][hapmap];0.80[AMR][1000 genomes]
rs62043869	0.88[AMR][1000 genomes]
rs62043871	0.89[AMR][1000 genomes]
rs62043872	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6493805	0.84[AMR][1000 genomes]
rs687128	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs71110312	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs715321	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7162071	0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7162879	0.82[JPT][hapmap]
rs7180112	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8031192	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8034113	0.80[AMR][1000 genomes]
rs8043521	0.82[ASN][1000 genomes]
rs9672390	0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9920076	0.80[CEU][hapmap];0.80[AMR][1000 genomes]
rs9920262	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12594642	MYO5C	cis	parietal	SCAN
rs12594642	CCPG1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55960800-55995800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:55987600-55995600	Weak transcription	Fetal Kidney	kidney
3	chr15:55987800-55996000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:55988000-55997200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:55988400-55995000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:55988400-55995600	Weak transcription	Hela-S3	cervix
7	chr15:55989800-55995800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:55992200-55995000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:55992600-55995000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:55993000-56003200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:55994000-55995000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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