Variant report

Variant	rs10020861
Chromosome Location	chr4:87777245-87777246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87769723..87774057-chr4:87775131..87777452,3	MCF-7	breast:
2	chr4:87776224..87780188-chr4:87811150..87813505,4	MCF-7	breast:
3	chr4:87755836..87758517-chr4:87776083..87778116,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145283	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10015508	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13106349	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13117771	1.00[ASN][1000 genomes]
rs13118214	1.00[ASN][1000 genomes]
rs13118640	1.00[ASN][1000 genomes]
rs13120839	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13126378	1.00[ASN][1000 genomes]
rs13137142	0.82[EUR][1000 genomes]
rs13138790	1.00[ASN][1000 genomes]
rs13138951	1.00[ASN][1000 genomes]
rs13141097	0.85[TSI][hapmap]
rs13141697	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16996065	1.00[CHB][hapmap]
rs17012114	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17012130	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2594281	0.95[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2594282	0.95[CEU][hapmap];1.00[EUR][1000 genomes]
rs2594284	0.95[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2705626	0.91[EUR][1000 genomes]
rs28378886	1.00[ASN][1000 genomes]
rs28401697	1.00[ASN][1000 genomes]
rs28450181	1.00[ASN][1000 genomes]
rs28495376	1.00[ASN][1000 genomes]
rs28533631	1.00[ASN][1000 genomes]
rs28574613	1.00[ASN][1000 genomes]
rs28633398	1.00[ASN][1000 genomes]
rs28682481	1.00[ASN][1000 genomes]
rs35606887	1.00[ASN][1000 genomes]
rs35635961	1.00[ASN][1000 genomes]
rs56414102	1.00[EUR][1000 genomes]
rs58866123	1.00[ASN][1000 genomes]
rs62305606	1.00[ASN][1000 genomes]
rs62305617	1.00[ASN][1000 genomes]
rs62305637	1.00[ASN][1000 genomes]
rs62305638	1.00[ASN][1000 genomes]
rs62305641	1.00[ASN][1000 genomes]
rs62305644	1.00[ASN][1000 genomes]
rs6811350	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6826767	1.00[ASN][1000 genomes]
rs727143	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7663218	0.82[EUR][1000 genomes]
rs7690165	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8180256	0.95[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9654158	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10020861	AFF1	cis	cerebellum	SCAN
rs10020861	PTPN13	cis	cerebellum	SCAN
rs10020861	PTPN13	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87769800-87778600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:87770400-87778600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:87771600-87785600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:87775800-87779200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:87776200-87778800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:87776200-87779000	Enhancers	HMEC	breast
7	chr4:87776200-87779200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:87776200-87779600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:87776400-87779200	Enhancers	NHEK	skin
10	chr4:87776400-87779600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:87776600-87778000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:87776600-87779000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:87776800-87777400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:87776800-87778200	Enhancers	NHDF-Ad	bronchial
15	chr4:87776800-87778600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:87776800-87778800	Enhancers	Hela-S3	cervix
17	chr4:87777000-87778600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:87777000-87778600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:87777200-87778400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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