Variant report

Variant	rs10249769
Chromosome Location	chr7:141089163-141089164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1007142	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1007143	0.81[AMR][1000 genomes]
rs10215677	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10245768	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10248336	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258367	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10258537	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261257	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10265432	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10274938	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1541419	0.81[AMR][1000 genomes]
rs17162203	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6953588	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6968682	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7811466	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917503	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs917504	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831160	chr7:141009011-141188046	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv34135	chr7:141047454-141492898	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv3429325	chr7:141064185-141196253	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv437577	chr7:141081752-141096047	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10249769	TAS2R38	cis	cerebellum	SCAN
rs10249769	OR9A2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:141086600-141097200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:141087400-141090800	Enhancers	Brain Germinal Matrix	brain
3	chr7:141087800-141095400	Weak transcription	Left Ventricle	heart
4	chr7:141088000-141089800	Weak transcription	Brain Anterior Caudate	brain
5	chr7:141088000-141090200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:141088200-141089400	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr7:141089000-141089400	Enhancers	Fetal Brain Male	brain
8	chr7:141089000-141089600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:141089000-141091000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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