Variant report

Variant	rs28662380
Chromosome Location	chr7:41259390-41259391
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10214983	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10215204	0.90[AMR][1000 genomes]
rs10225596	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10228281	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10237505	0.90[AMR][1000 genomes]
rs10244988	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10245806	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10245865	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10255353	0.81[AMR][1000 genomes]
rs10260526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266295	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17691173	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17691214	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158559	0.81[AMR][1000 genomes]
rs28370881	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28482024	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs28534868	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28537692	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28689699	0.81[AMR][1000 genomes]
rs4296946	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58052804	0.81[AMR][1000 genomes]
rs58773259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58811351	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59159806	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59455753	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60824519	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61187499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61586765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951284	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73687949	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73687950	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][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

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41257400-41262400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:41257800-41261600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:41257800-41261800	Weak transcription	HMEC	breast
4	chr7:41258200-41259800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:41258600-41259400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:41258600-41259800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:41258600-41260400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr7:41258800-41259400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr7:41258800-41259400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
10	chr7:41258800-41259400	Enhancers	HSMM	muscle
11	chr7:41258800-41259600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:41259000-41259400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr7:41259000-41259400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:41259000-41259400	Enhancers	NH-A	brain
15	chr7:41259200-41261800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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