Variant report

Variant	rs664628
Chromosome Location	chr3:43097710-43097711
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	chr3:43092511..43095463-chr3:43096998..43098764,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13061038	0.89[EUR][1000 genomes]
rs13095711	0.97[EUR][1000 genomes]
rs2936817	0.92[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs3732856	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs476336	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509527	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs517650	0.88[CEU][hapmap]
rs536572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs565521	0.88[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs590899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606724	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62247065	0.87[EUR][1000 genomes]
rs643663	0.90[EUR][1000 genomes]
rs658958	0.92[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs660324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806706	0.92[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs693290	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697327	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs704912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs834178	0.85[CEU][hapmap]
rs834188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs834191	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs870238	0.92[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9311333	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs9882262	0.88[CEU][hapmap];0.90[EUR][1000 genomes]

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
rs664628	C3orf39	cis	parietal	SCAN
rs664628	LYZL4	cis	cerebellum	SCAN
rs664628	CCR9	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43092200-43101000	Weak transcription	Pancreas	Pancrea
2	chr3:43092800-43117800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:43094200-43099800	Weak transcription	Adipose Nuclei	Adipose
5	chr3:43094200-43104200	Weak transcription	Gastric	stomach
6	chr3:43094400-43101400	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:43094400-43101800	Weak transcription	Placenta	Placenta
8	chr3:43094400-43114800	Weak transcription	Brain Anterior Caudate	brain
9	chr3:43095000-43101000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:43095000-43114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:43095600-43098200	Strong transcription	Stomach Smooth Muscle	stomach
12	chr3:43095600-43098400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:43095600-43100000	Weak transcription	Fetal Intestine Small	intestine
14	chr3:43095800-43101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:43095800-43104400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:43096800-43098000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:43096800-43100200	Strong transcription	Liver	Liver
19	chr3:43096800-43102600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:43097000-43098000	Strong transcription	Fetal Stomach	stomach
21	chr3:43097200-43099600	Weak transcription	Lung	lung
22	chr3:43097200-43104600	Weak transcription	Brain Substantia Nigra	brain
23	chr3:43097600-43098000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr3:43097600-43098800	Strong transcription	Ovary	ovary
25	chr3:43097600-43101000	Weak transcription	Fetal Muscle Leg	muscle

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