Variant report

Variant	rs10946675
Chromosome Location	chr6:24141920-24141921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1053047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12190150	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211300	0.81[CEU][hapmap]
rs13203341	0.81[EUR][1000 genomes]
rs28385635	0.85[EUR][1000 genomes]
rs3178	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36060488	0.83[EUR][1000 genomes]
rs3857540	0.81[EUR][1000 genomes]
rs4582376	0.81[CEU][hapmap];0.85[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10946675	HIST1H3G	cis	cerebellum	SCAN
rs10946675	KAAG1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24127600-24146800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:24140400-24142200	Enhancers	Fetal Muscle Leg	muscle
3	chr6:24140600-24142000	Enhancers	Brain Angular Gyrus	brain
4	chr6:24140600-24142000	Enhancers	Brain Germinal Matrix	brain
5	chr6:24140600-24142000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:24140600-24142200	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr6:24140600-24142200	Enhancers	Fetal Lung	lung
8	chr6:24140600-24145600	Weak transcription	HepG2	liver
9	chr6:24141000-24142000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:24141000-24142000	Enhancers	Brain Cingulate Gyrus	brain
11	chr6:24141000-24142000	Enhancers	Fetal Brain Male	brain
12	chr6:24141200-24142200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr6:24141200-24142200	Enhancers	Rectal Smooth Muscle	rectum
14	chr6:24141400-24142000	Enhancers	Brain Hippocampus Middle	brain
15	chr6:24141600-24145800	Weak transcription	Brain Anterior Caudate	brain
16	chr6:24141800-24144200	Weak transcription	Fetal Brain Female	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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