Variant report

Variant	rs3857540
Chromosome Location	chr6:24158542-24158543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1053047	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10946675	0.89[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs10946679	0.82[JPT][hapmap]
rs12190150	0.81[EUR][1000 genomes]
rs12211300	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13203341	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1832708	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28385635	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3178	0.82[EUR][1000 genomes]
rs36060488	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4582376	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	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
2	esv1798372	chr6:24158542-24181477	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3857540	BTN3A3	cis	cerebellum	SCAN
rs3857540	KAAG1	cis	parietal	SCAN
rs3857540	HIST1H3G	cis	cerebellum	SCAN
rs3857540	NUMB	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24153800-24200800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:24155600-24160400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:24156400-24159000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:24157000-24158800	Enhancers	Brain Germinal Matrix	brain
5	chr6:24157600-24158800	Enhancers	Fetal Lung	lung
6	chr6:24157800-24158600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr6:24158000-24158600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:24158000-24158600	Enhancers	Rectal Smooth Muscle	rectum

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

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