Variant report

Variant	rs2006301
Chromosome Location	chr22:31465217-31465218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31464585..31466786-chr22:31479626..31481207,2	MCF-7	breast:
2	chr22:31450083..31452668-chr22:31463620..31466392,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183963	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10427701	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10854603	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11705177	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11705250	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11705252	0.87[AFR][1000 genomes]
rs11705313	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11705319	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11705369	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11705396	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12157450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12165471	1.00[ASN][1000 genomes]
rs12168052	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12170984	0.97[ASN][1000 genomes]
rs12330058	0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs13057068	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240430	0.84[CHD][hapmap]
rs35060453	1.00[ASN][1000 genomes]
rs5021960	0.82[AMR][1000 genomes]
rs5749210	0.80[EUR][1000 genomes]
rs5753433	0.84[CEU][hapmap]
rs5753434	0.84[CEU][hapmap]
rs5753436	0.84[CEU][hapmap]
rs5753438	0.80[EUR][1000 genomes]
rs5994365	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5994366	1.00[JPT][hapmap]
rs5994368	1.00[ASN][1000 genomes]
rs5994370	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5997863	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997864	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997866	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997871	0.90[ASN][1000 genomes]
rs5997872	0.84[CEU][hapmap];0.84[CHD][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs715297	1.00[JPT][hapmap]
rs7284593	1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7285683	1.00[JPT][hapmap]
rs7287041	0.88[AFR][1000 genomes]
rs7291565	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7292038	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7292982	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs736901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9619166	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9619167	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9621175	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv20214	chr22:31461316-31474644	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1000178	chr22:31461678-31474550	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2006301	SEC14L4	cis	cerebellum	SCAN
rs2006301	SEZ6L	cis	parietal	SCAN
rs2006301	HSCB	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31457000-31465400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr22:31461200-31465400	Weak transcription	HepG2	liver
3	chr22:31464400-31465600	Weak transcription	A549	lung
4	chr22:31464800-31465400	Enhancers	Fetal Intestine Large	intestine
5	chr22:31464800-31465600	Enhancers	Fetal Intestine Small	intestine
6	chr22:31465000-31465800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:31465000-31466200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr22:31465200-31466200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr22:31465200-31466400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links