Variant report

Variant	rs1303845
Chromosome Location	chr22:28722535-28722536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs134172	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs134179	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs134180	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs134183	0.95[CEU][hapmap]
rs134188	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs134196	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs134489	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs134491	0.81[EUR][1000 genomes]
rs134500	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs134507	1.00[CEU][hapmap];0.92[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs134526	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs134541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs134543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs134548	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs134551	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17503350	0.95[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2223370	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2346397	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs4822952	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs5752743	0.85[JPT][hapmap]
rs5762629	0.83[CEU][hapmap]
rs5762660	0.85[JPT][hapmap]
rs695591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs695625	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs695796	0.80[ASN][1000 genomes]
rs695797	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs715517	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7284814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs7288403	1.00[YRI][hapmap]
rs8140229	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1303845	SUSD2	cis	parietal	SCAN
rs1303845	SEC14L4	cis	parietal	SCAN
rs1303845	TTC28	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28712200-28725600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:28716400-28722600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr22:28717200-28726400	Weak transcription	Brain Germinal Matrix	brain
4	chr22:28720200-28724800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links