Variant report

Variant	rs2684943
Chromosome Location	chr15:34333001-34333002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:34332569-34333265	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:34330080-34333046	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34330950..34333091-chr15:34501411..34503652,2	K562	blood:
2	chr15:34332870..34334555-chr15:34335095..34337616,2	MCF-7	breast:

Variant related genes	Relation type
AVEN	TF binding region
ENSG00000134152	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12902762	0.81[ASN][1000 genomes]
rs1872806	0.86[ASN][1000 genomes]
rs2078561	0.85[ASN][1000 genomes]
rs2078562	0.86[ASN][1000 genomes]
rs2243858	0.86[ASN][1000 genomes]
rs2632075	0.86[ASN][1000 genomes]
rs2632076	0.81[ASN][1000 genomes]
rs2632078	0.86[ASN][1000 genomes]
rs2632079	0.86[ASN][1000 genomes]
rs2632107	0.86[ASN][1000 genomes]
rs2684931	0.86[ASN][1000 genomes]
rs2684932	0.86[ASN][1000 genomes]
rs2684939	0.94[ASN][1000 genomes]
rs2684941	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2684956	0.81[ASN][1000 genomes]
rs2702278	0.84[ASN][1000 genomes]
rs2702281	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2702282	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2702284	0.86[ASN][1000 genomes]
rs2702285	0.86[ASN][1000 genomes]
rs2702306	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28667556	0.81[ASN][1000 genomes]
rs3861194	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs481391	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5016373	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs543621	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55805034	0.87[ASN][1000 genomes]
rs613479	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs625596	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs682052	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8040776	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs893138	0.80[AFR][1000 genomes];0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2684943	ENSG00000169857	cis	multi-tissue	Pritchard
rs2684943	AVEN	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34332000-34339000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:34332200-34333800	Enhancers	Fetal Heart	heart
3	chr15:34332200-34337400	Weak transcription	HSMM	muscle
4	chr15:34332200-34339400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:34332400-34333600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:34332400-34335600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:34332400-34335600	Weak transcription	Osteobl	bone
8	chr15:34332400-34335800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:34332400-34337400	Weak transcription	HSMMtube	muscle
10	chr15:34332400-34337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:34332400-34337600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:34332400-34338000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:34332600-34337600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:34332800-34335600	Weak transcription	NH-A	brain
15	chr15:34332800-34335800	Weak transcription	HepG2	liver
16	chr15:34333000-34335600	Weak transcription	GM12878-XiMat	blood

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