Variant report

Variant	rs675996
Chromosome Location	chr15:42400764-42400765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1668549	0.93[ASN][1000 genomes]
rs2122676	0.88[ASN][1000 genomes]
rs2167294	0.88[ASN][1000 genomes]
rs2280248	0.85[CHB][hapmap]
rs2412669	0.88[ASN][1000 genomes]
rs2677756	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28414830	0.88[ASN][1000 genomes]
rs28499088	0.88[ASN][1000 genomes]
rs28665345	0.88[ASN][1000 genomes]
rs28718476	0.88[ASN][1000 genomes]
rs55926717	0.86[ASN][1000 genomes]
rs56040775	0.88[ASN][1000 genomes]
rs58905750	0.88[ASN][1000 genomes]
rs600957	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60279267	0.88[ASN][1000 genomes]
rs60513852	0.88[ASN][1000 genomes]
rs60759517	0.88[ASN][1000 genomes]
rs60807341	0.89[ASN][1000 genomes]
rs61190589	0.88[ASN][1000 genomes]
rs635548	0.85[CHB][hapmap]
rs6650522	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72489213	0.88[ASN][1000 genomes]
rs74011727	0.88[ASN][1000 genomes]
rs74011729	0.88[ASN][1000 genomes]
rs74011732	0.84[ASN][1000 genomes]
rs776716	0.94[ASN][1000 genomes]
rs776718	0.85[ASN][1000 genomes]
rs8023346	0.88[ASN][1000 genomes]
rs8030796	0.88[ASN][1000 genomes]
rs8032387	0.88[ASN][1000 genomes]
rs8042280	0.88[ASN][1000 genomes]
rs9672757	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv457121	chr15:42396282-42418085	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv569236	chr15:42396282-42418085	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs675996	VPS39	cis	cerebellum	SCAN
rs675996	ADAL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42395200-42404000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:42396200-42404200	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr15:42396200-42405200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr15:42397800-42402200	Weak transcription	Dnd41	blood
5	chr15:42398000-42400800	Bivalent Enhancer	HepG2	liver
6	chr15:42399000-42400800	Enhancers	Gastric	stomach
7	chr15:42399600-42400800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:42399600-42400800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:42400000-42402400	Weak transcription	Lung	lung
10	chr15:42400000-42402600	Weak transcription	Stomach Mucosa	stomach
11	chr15:42400000-42404200	Weak transcription	Esophagus	oesophagus
12	chr15:42400200-42401200	Weak transcription	Fetal Thymus	thymus
13	chr15:42400400-42401400	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr15:42400400-42403400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr15:42400600-42401600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:42400600-42404400	Weak transcription	Rectal Mucosa Donor 31	rectum

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