Variant report

Variant	rs3935572
Chromosome Location	chr5:147524833-147524834
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	chr5:147514157..147516994-chr5:147523007..147525747,2	MCF-7	breast:
2	chr5:147523792..147526383-chr5:147529458..147531913,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10061827	0.92[AFR][1000 genomes]
rs10065999	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs10067334	0.81[CEU][hapmap]
rs10068913	0.83[CHB][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs10068916	0.82[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10068988	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs10070470	0.92[AFR][1000 genomes]
rs10075227	0.92[AFR][1000 genomes]
rs11168034	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13165271	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13169394	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13360182	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs1974627	0.85[AFR][1000 genomes]
rs2191680	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2400488	0.92[AFR][1000 genomes]
rs2400491	0.92[AFR][1000 genomes]
rs2400492	0.92[AFR][1000 genomes]
rs2400493	0.85[AFR][1000 genomes]
rs2400496	0.85[AFR][1000 genomes]
rs4254894	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[YRI][hapmap]
rs4269285	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4270684	0.85[AFR][1000 genomes]
rs4419576	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4452547	0.88[AFR][1000 genomes]
rs6881658	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs6888999	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6895745	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap]
rs724726	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs767569	0.85[AFR][1000 genomes]
rs767570	0.85[AFR][1000 genomes]
rs7717500	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9285669	0.86[AFR][1000 genomes]
rs9325077	0.92[AFR][1000 genomes]
rs9325078	0.92[AFR][1000 genomes]
rs9325084	0.88[AFR][1000 genomes]
rs9885451	0.82[CEU][hapmap]

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	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3935572	SPINK6	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147487800-147525800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:147502400-147526000	Weak transcription	Hela-S3	cervix
3	chr5:147513600-147526200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:147515200-147525400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:147515800-147525200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:147517200-147525400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:147522000-147526000	Weak transcription	Pancreas	Pancrea
8	chr5:147524000-147526200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr5:147524000-147528200	Enhancers	Stomach Mucosa	stomach
10	chr5:147524200-147526600	Enhancers	HUVEC	blood vessel
11	chr5:147524400-147525000	Enhancers	Fetal Intestine Large	intestine
12	chr5:147524400-147525200	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr5:147524600-147525800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:147524600-147527800	Enhancers	HepG2	liver
15	chr5:147524600-147528000	Enhancers	Fetal Intestine Small	intestine
16	chr5:147524800-147526200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:147524800-147526200	Enhancers	Fetal Lung	lung

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