Variant report

Variant	rs10235458
Chromosome Location	chr7:40862370-40862371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1006376	0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1013574	0.81[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs10225209	0.87[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10225445	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10226900	1.00[YRI][hapmap]
rs10231545	0.80[YRI][hapmap];0.83[AFR][1000 genomes]
rs10233069	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10243080	0.90[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10252053	1.00[YRI][hapmap]
rs10268219	0.83[LWK][hapmap]
rs10272186	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10276001	0.81[AFR][1000 genomes]
rs10276629	0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1029620	0.85[ASN][1000 genomes]
rs1029621	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951639	0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1203569	0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12537964	0.82[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs12666544	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12701835	0.83[AFR][1000 genomes]
rs13243593	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13246232	0.86[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs17621030	0.90[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17688285	0.83[AFR][1000 genomes]
rs17688414	0.85[AFR][1000 genomes]
rs17770843	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17770991	0.83[LWK][hapmap]
rs1921743	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1921745	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1921746	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs1921747	0.80[YRI][hapmap];0.83[AFR][1000 genomes]
rs1921748	0.89[YRI][hapmap]
rs2108375	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2108376	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2302025	0.83[LWK][hapmap]
rs2302026	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2329877	0.82[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs34565813	0.92[ASN][1000 genomes]
rs34689844	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs35146091	0.88[AFR][1000 genomes]
rs35712272	0.87[AFR][1000 genomes]
rs35995194	0.85[ASN][1000 genomes]
rs3815265	1.00[YRI][hapmap]
rs4723979	0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs59027414	0.98[EUR][1000 genomes]
rs62449401	0.89[AFR][1000 genomes]
rs62449405	0.98[EUR][1000 genomes]
rs62449407	0.98[EUR][1000 genomes]
rs6462989	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs68023334	0.89[AFR][1000 genomes]
rs6949092	0.92[ASN][1000 genomes]
rs723838	0.83[ASN][1000 genomes]
rs73125791	0.99[EUR][1000 genomes]
rs7784052	0.98[EUR][1000 genomes]
rs7801192	0.84[AFR][1000 genomes]
rs7808211	0.80[YRI][hapmap]
rs886831	0.90[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][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	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830972	chr7:40814709-40945917	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1827128	chr7:40862370-40886576	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10235458	STK33	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40855200-40864000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:40855600-40862400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:40855600-40866000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:40855800-40866200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:40856400-40865200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:40857000-40863600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:40858000-40862400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:40858000-40864200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:40858200-40863400	Weak transcription	NHEK	skin
10	chr7:40858200-40863800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:40861200-40865600	Weak transcription	HSMMtube	muscle
12	chr7:40862200-40862800	Enhancers	Osteobl	bone
13	chr7:40862200-40863000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:40862200-40863200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:40862200-40863200	Enhancers	Fetal Heart	heart
16	chr7:40862200-40867800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:40862200-40868200	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links