Variant report

Variant	rs4779656
Chromosome Location	chr15:34324603-34324604
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	chr15:34323079..34325839-chr15:34329919..34331772,2	K562	blood:

Variant related genes	Relation type
ENSG00000169857	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11072868	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635479	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898898	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903907	0.95[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs12913747	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078562	1.00[YRI][hapmap]
rs2243858	1.00[YRI][hapmap]
rs2339352	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632075	1.00[YRI][hapmap]
rs2632076	1.00[YRI][hapmap]
rs2684931	1.00[YRI][hapmap]
rs2684932	0.88[YRI][hapmap]
rs2684940	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684953	1.00[YRI][hapmap]
rs2702284	1.00[YRI][hapmap]
rs2702285	1.00[YRI][hapmap]
rs2705338	0.86[TSI][hapmap]
rs34474029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34773983	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35804445	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779652	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532720	0.85[CEU][hapmap]
rs536345	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602302	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618868	0.88[EUR][1000 genomes]
rs62014670	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62014671	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs632591	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495442	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495443	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66530874	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67739072	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71462883	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71464844	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7162140	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168640	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7169003	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173183	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175823	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175933	0.80[TSI][hapmap]
rs7178075	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178446	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72718678	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72718682	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030094	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033781	0.84[AMR][1000 genomes];0.80[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4779656	NDNL2	cis	parietal	SCAN
rs4779656	AVEN	cis	multi-tissue	Pritchard
rs4779656	CHRM5	cis	parietal	SCAN
rs4779656	RYR3	cis	parietal	SCAN
rs4779656	AVEN	Cis_1M	lymphoblastoid	RTeQTL
rs4779656	CHRM5	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34309400-34330000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:34309600-34330000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:34314200-34326400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:34316600-34329400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:34320200-34329800	Weak transcription	Hela-S3	cervix
6	chr15:34320400-34326400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:34320600-34327000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:34323000-34328000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:34323000-34330000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:34324200-34325000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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