Variant report

Variant	rs3856636
Chromosome Location	chr3:138025136-138025137
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138016564..138021250-chr3:138021841..138026048,7	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13087441	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[MEX][hapmap]
rs2291093	0.83[JPT][hapmap]
rs3732840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3773763	0.89[ASN][1000 genomes]
rs3856633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4678406	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6778511	0.81[JPT][hapmap]
rs6805348	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637162	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7638688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289556	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9846480	0.91[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs9846722	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9867678	0.80[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3856636	SR140	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137982000-138026600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:138005400-138027000	Weak transcription	Fetal Heart	heart
3	chr3:138017800-138025200	Weak transcription	Aorta	Aorta
4	chr3:138017800-138025600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:138018200-138026200	Weak transcription	HSMMtube	muscle
6	chr3:138018200-138026400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:138018200-138026400	Weak transcription	Primary T cells from cord blood	blood
8	chr3:138018200-138042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:138018600-138025600	Weak transcription	Thymus	Thymus
10	chr3:138019000-138025200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:138019000-138025600	Weak transcription	Fetal Stomach	stomach
12	chr3:138019000-138025800	Weak transcription	Brain Germinal Matrix	brain
13	chr3:138019000-138026800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:138019200-138025400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:138019600-138025400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:138023200-138026800	Weak transcription	Brain Anterior Caudate	brain
17	chr3:138024000-138025200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:138024000-138031400	Weak transcription	Pancreas	Pancrea
19	chr3:138024200-138026800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:138025000-138026200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links