Variant report

Variant	rs4774802
Chromosome Location	chr15:56000470-56000471
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	chr15:55999212..56002187-chr15:56002535..56005637,3	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10518817	0.86[CHB][hapmap]
rs10851589	0.86[CHB][hapmap]
rs10851591	0.98[ASN][1000 genomes]
rs11630141	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854213	0.85[CHB][hapmap]
rs11858195	0.81[JPT][hapmap];0.84[MEX][hapmap]
rs12373006	0.90[CHB][hapmap]
rs12438177	0.80[CHB][hapmap]
rs12442771	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591246	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12592192	0.81[ASN][1000 genomes]
rs12903822	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs12908232	0.80[CEU][hapmap]
rs16976450	0.81[CHB][hapmap]
rs16976472	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1814329	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2008336	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2118781	0.85[CHB][hapmap]
rs2414424	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2414426	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2414427	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2414430	0.86[ASN][1000 genomes]
rs2414431	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs28485308	0.90[ASN][1000 genomes]
rs28575567	0.89[ASN][1000 genomes]
rs4377101	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs4774803	0.97[ASN][1000 genomes]
rs62043871	0.80[ASN][1000 genomes]
rs62043872	0.86[ASN][1000 genomes]
rs6493807	0.80[ASN][1000 genomes]
rs6493809	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6493814	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs687128	1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71110312	0.89[ASN][1000 genomes]
rs715321	0.87[ASN][1000 genomes]
rs7161967	0.91[ASN][1000 genomes]
rs7162071	0.85[YRI][hapmap]
rs7162371	0.98[ASN][1000 genomes]
rs7162879	0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7163167	0.85[CHB][hapmap]
rs7171318	0.86[CHB][hapmap]
rs7172903	0.80[ASN][1000 genomes]
rs7178379	0.86[CHB][hapmap]
rs7180112	0.80[ASN][1000 genomes]
rs7181212	0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7182733	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7359255	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8023911	0.89[ASN][1000 genomes]
rs8025445	0.85[CHB][hapmap]
rs8031192	0.81[JPT][hapmap]
rs8034414	0.96[ASN][1000 genomes]
rs8037136	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs8042029	0.92[ASN][1000 genomes]
rs9920246	0.82[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4774802	CCPG1	cis	parietal	SCAN
rs4774802	AP4E1	cis	parietal	SCAN
rs4774802	MYO5C	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55993000-56003200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:55995000-56000800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:55996200-56015000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:55996400-56003400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:55996400-56007600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:55996600-56004800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:55996600-56005400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:55996800-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:55997000-56002200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:55998400-56001400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:55999000-56000600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:55999000-56005000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:55999200-56001800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:55999400-56001000	Enhancers	Hela-S3	cervix
15	chr15:55999600-56001200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:55999800-56028000	Weak transcription	Fetal Kidney	kidney

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