Variant report

Variant	rs536119
Chromosome Location	chr3:43095101-43095102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43060384..43063031-chr3:43093535..43095957,2	K562	blood:
2	chr3:43092511..43095463-chr3:43096998..43098764,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF662-1	chr3:43095013-43095766	NONHSAT089276

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13095711	0.87[ASN][1000 genomes]
rs2280565	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2936817	0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs34970115	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35339908	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732856	0.80[CHD][hapmap]
rs473467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477594	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496436	0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs504973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56009835	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs601055	0.89[MKK][hapmap]
rs606336	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs643663	0.84[ASN][1000 genomes]
rs648273	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs658958	0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs660446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686464	0.83[YRI][hapmap]
rs697327	0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs870238	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs9311333	0.84[JPT][hapmap]
rs9882262	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs536119	C3orf39	cis	parietal	SCAN
rs536119	LYZL4	cis	cerebellum	SCAN
rs536119	CCDC13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43085000-43097600	Weak transcription	Ovary	ovary
2	chr3:43092200-43101000	Weak transcription	Pancreas	Pancrea
3	chr3:43092400-43096800	Weak transcription	Liver	Liver
4	chr3:43092800-43117800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:43094200-43099800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:43094200-43104200	Weak transcription	Gastric	stomach
8	chr3:43094400-43101400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:43094400-43101800	Weak transcription	Placenta	Placenta
10	chr3:43094400-43114800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:43094800-43095200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr3:43094800-43095600	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr3:43094800-43095600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:43095000-43095800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:43095000-43101000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:43095000-43114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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