Variant report

Variant	rs4778909
Chromosome Location	chr15:79155088-79155089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:79147722..79157046-chr15:79163022..79167664,11	K562	blood:
2	chr15:79152585..79155864-chr15:79171888..79174971,4	K562	blood:
3	chr15:79149764..79156555-chr15:79163462..79168215,14	K562	blood:

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10444811	0.84[CEU][hapmap]
rs10519215	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs10519216	0.84[CEU][hapmap]
rs10519217	0.84[CEU][hapmap]
rs10519219	0.84[CEU][hapmap]
rs11857042	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12050510	0.81[CEU][hapmap]
rs12050511	0.83[CEU][hapmap]
rs12438191	0.90[ASN][1000 genomes]
rs12438433	0.84[CEU][hapmap]
rs12439583	0.84[CEU][hapmap]
rs12440662	0.85[EUR][1000 genomes]
rs12442036	0.85[EUR][1000 genomes]
rs12442152	1.00[EUR][1000 genomes]
rs12443105	0.84[CEU][hapmap]
rs12592618	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12916055	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16970223	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16970244	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1836556	0.83[CEU][hapmap]
rs2289700	0.84[CHD][hapmap]
rs4622479	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4624135	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4628930	0.85[EUR][1000 genomes]
rs4778738	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4778740	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56031815	0.83[EUR][1000 genomes]
rs56225615	0.85[EUR][1000 genomes]
rs58848937	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61157089	1.00[EUR][1000 genomes]
rs62011027	0.85[EUR][1000 genomes]
rs62011029	0.85[EUR][1000 genomes]
rs62011032	0.85[EUR][1000 genomes]
rs62011033	0.85[EUR][1000 genomes]
rs62011034	0.85[EUR][1000 genomes]
rs62011036	0.88[EUR][1000 genomes]
rs62011050	1.00[EUR][1000 genomes]
rs62011052	0.98[EUR][1000 genomes]
rs62013196	0.90[ASN][1000 genomes]
rs6495343	0.85[EUR][1000 genomes]
rs7165139	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174727	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs7179763	0.84[CEU][hapmap]
rs7181240	0.85[EUR][1000 genomes]
rs7497610	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8028352	0.97[ASN][1000 genomes]
rs8029496	0.84[CEU][hapmap]
rs8037651	0.84[CEU][hapmap]
rs8039140	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8039144	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4778909	CSK	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79153000-79163200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr15:79153200-79156200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:79153200-79163200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:79153200-79164600	Weak transcription	A549	lung
5	chr15:79153600-79156800	Weak transcription	HepG2	liver

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