Variant report

Variant	rs613479
Chromosome Location	chr15:34359190-34359191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34354339..34357870-chr15:34358322..34362266,6	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11857888	0.83[ASN][1000 genomes]
rs12902762	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1872806	0.83[ASN][1000 genomes]
rs2078561	0.82[ASN][1000 genomes]
rs2078562	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2243858	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2632075	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2632076	0.87[CHB][hapmap]
rs2632078	0.83[ASN][1000 genomes]
rs2632079	0.83[ASN][1000 genomes]
rs2632107	0.83[ASN][1000 genomes]
rs2684931	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2684932	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2684939	0.89[ASN][1000 genomes]
rs2684941	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2684943	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2702278	0.82[ASN][1000 genomes]
rs2702281	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2702282	0.84[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2702284	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2702285	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2702306	0.90[ASN][1000 genomes]
rs28432827	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28667556	0.86[ASN][1000 genomes]
rs34571863	0.83[ASN][1000 genomes]
rs3794592	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3861194	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs481391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489832	1.00[ASW][hapmap];0.91[LWK][hapmap]
rs5016373	0.84[ASN][1000 genomes]
rs511422	1.00[ASW][hapmap];0.91[LWK][hapmap]
rs522397	0.92[CEU][hapmap]
rs543621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55747528	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55805034	0.83[ASN][1000 genomes]
rs588655	1.00[ASW][hapmap]
rs623941	0.92[CEU][hapmap]
rs625596	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636842	1.00[ASW][hapmap]
rs682052	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8029961	0.82[CHB][hapmap]
rs8030334	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs8040776	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs893138	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[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	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv903985	chr15:34279319-34370487	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs613479	PGBD4	cis	parietal	SCAN
rs613479	CHRM5	cis	cerebellum	SCAN
rs613479	AVEN	cis	lymphoblastoid	seeQTL
rs613479	CHRM5	cis	parietal	SCAN
rs613479	AVEN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34354200-34372400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:34354200-34375600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:34354200-34376400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:34354400-34379600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:34355000-34369000	Weak transcription	Liver	Liver
6	chr15:34358600-34393000	Weak transcription	Aorta	Aorta

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