Variant report

Variant	rs1326837
Chromosome Location	chr10:96386206-96386207
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	chr10:96384761..96386735-chr10:96941217..96943673,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225533	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1010570	0.87[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10736086	1.00[JPT][hapmap]
rs12762067	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12772169	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12772521	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1575934	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1926706	0.83[ASN][1000 genomes]
rs1998591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2094296	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2104161	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2104543	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2281889	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2901783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34195517	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34367065	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34870400	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4362080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4501922	0.82[AMR][1000 genomes]
rs67482845	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68157779	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs749744	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7912099	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7914753	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7916649	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv517681	chr10:96343228-96387079	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1326837	HELLS	cis	cerebellum	SCAN
rs1326837	C10orf28	cis	cerebellum	SCAN
rs1326837	KIF11	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96383000-96386600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:96383000-96387400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:96383400-96387800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:96383600-96389800	Weak transcription	Fetal Intestine Large	intestine
5	chr10:96383800-96388800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:96384400-96387400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr10:96386200-96386600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:96386200-96386800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr10:96386200-96386800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:96386200-96386800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:96386200-96386800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr10:96386200-96386800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr10:96386200-96386800	Enhancers	HSMM	muscle
14	chr10:96386200-96387400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr10:96386200-96387600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr10:96386200-96387600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr10:96386200-96387600	Enhancers	NHEK	skin
18	chr10:96386200-96388000	Enhancers	HUES6 Cell Line	embryonic stem cell

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