Variant report

Variant	rs704912
Chromosome Location	chr3:43084131-43084132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs476336	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs509527	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs517650	0.88[CEU][hapmap]
rs536572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs565521	0.88[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs590899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs606724	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62247065	0.88[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs664628	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]
rs6806706	0.92[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs693290	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs697327	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs834178	0.85[CEU][hapmap]
rs834188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs834191	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs870238	0.92[CEU][hapmap];0.87[TSI][hapmap];0.90[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
rs704912	LYZL4	cis	cerebellum	SCAN
rs704912	CCR9	cis	parietal	SCAN
rs704912	C3orf39	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43059600-43084600	Weak transcription	Pancreas	Pancrea
2	chr3:43063600-43084800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:43065400-43084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:43070600-43084800	Weak transcription	Esophagus	oesophagus
5	chr3:43073400-43084600	Weak transcription	Brain Angular Gyrus	brain
6	chr3:43073400-43084600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:43073600-43084400	Weak transcription	Adipose Nuclei	Adipose
8	chr3:43074600-43084200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:43075200-43084200	Weak transcription	Ovary	ovary
10	chr3:43077200-43084400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:43077600-43084600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:43078400-43084200	Weak transcription	Placenta	Placenta
13	chr3:43078800-43084200	Weak transcription	Liver	Liver
14	chr3:43078800-43084400	Weak transcription	Fetal Stomach	stomach
15	chr3:43079000-43085400	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:43080200-43091000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:43083400-43085800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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