Variant report

Variant	rs10215204
Chromosome Location	chr7:41293607-41293608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10214983	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10225596	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10228281	0.90[AMR][1000 genomes]
rs10237505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10244988	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10245806	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10245865	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10255353	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10260526	0.90[AMR][1000 genomes]
rs10266295	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10266444	0.91[EUR][1000 genomes]
rs17691173	0.87[AMR][1000 genomes]
rs17691214	0.87[AMR][1000 genomes]
rs2158559	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28370881	0.85[AMR][1000 genomes]
rs28482024	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28534868	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28537692	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28662380	0.90[AMR][1000 genomes]
rs28689699	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58773259	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58811351	0.80[EUR][1000 genomes]
rs59159806	0.87[AMR][1000 genomes]
rs60824519	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61187499	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61586765	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6951284	0.87[AMR][1000 genomes]
rs73687949	0.88[AMR][1000 genomes]
rs73687950	0.87[AMR][1000 genomes]
rs73687979	0.80[AFR][1000 genomes]
rs73687980	0.80[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	nsv887989	chr7:41125447-41337044	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1028983	chr7:41165668-41635954	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv534465	chr7:41224437-41443498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10215204	TBRG4	cis	cerebellum	SCAN
rs10215204	NPC1L1	cis	parietal	SCAN
rs10215204	MYL7	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41265000-41296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:41288000-41296200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:41291600-41294400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:41291800-41295800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:41291800-41296200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:41292400-41295800	Weak transcription	HMEC	breast
7	chr7:41293000-41295800	Weak transcription	NHEK	skin

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