Variant report

Variant	rs6777886
Chromosome Location	chr3:141042222-141042223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:141042116-141042405	K562	blood:	n/a	chr3:141042216-141042229

No.	Distal block	Cell Line	Cell type
1	chr3:141041261..141045456-chr3:141085742..141089187,4	K562	blood:
2	chr3:141041057..141042632-chr3:141043258..141046046,3	K562	blood:
3	chr3:141040944..141042691-chr3:141048357..141050949,3	K562	blood:
4	chr3:141041261..141043649-chr3:141085742..141087985,3	K562	blood:

Variant related genes	Relation type
ZBTB38	TF binding region
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1511380	0.87[ASW][hapmap];1.00[CHD][hapmap];0.89[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs17787621	1.00[ASN][1000 genomes]
rs1983235	0.96[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4132036	1.00[ASN][1000 genomes]
rs4325905	0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs56054141	1.00[ASN][1000 genomes]
rs59539710	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6765857	0.87[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6771916	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6795197	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795377	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616781	0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs7636469	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829470	0.91[YRI][hapmap]
rs9843461	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6777886	RASA2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141031800-141047400	Weak transcription	Right Ventricle	heart
2	chr3:141039600-141042800	Enhancers	Fetal Intestine Large	intestine
3	chr3:141039800-141042800	Enhancers	Fetal Intestine Small	intestine
4	chr3:141040000-141042800	Weak transcription	K562	blood
5	chr3:141040200-141042400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:141040200-141044000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:141040200-141044600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:141040200-141045200	Weak transcription	Lung	lung
9	chr3:141040400-141042800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:141040400-141043000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:141040600-141045200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:141040600-141049000	Weak transcription	Hela-S3	cervix
13	chr3:141040600-141049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:141040800-141044800	Weak transcription	HUVEC	blood vessel
15	chr3:141041200-141043000	Weak transcription	Small Intestine	intestine
16	chr3:141041400-141044800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:141042000-141042800	Enhancers	Duodenum Mucosa	Duodenum
18	chr3:141042000-141043000	Enhancers	HepG2	liver
19	chr3:141042000-141043400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:141042200-141043200	Enhancers	Fetal Kidney	kidney
21	chr3:141042200-141044200	Enhancers	A549	lung

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