Variant report

Variant	rs3860901
Chromosome Location	chr9:85959817-85959818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10117284	0.80[TSI][hapmap]
rs10125561	1.00[ASN][1000 genomes]
rs10867997	0.99[ASN][1000 genomes]
rs12349789	0.80[TSI][hapmap]
rs2375922	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3860902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3860912	0.88[GIH][hapmap];0.90[TSI][hapmap]
rs3904187	0.81[CHD][hapmap];0.80[TSI][hapmap]
rs4085854	0.88[ASN][1000 genomes]
rs4297106	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs4478644	0.88[GIH][hapmap];0.90[TSI][hapmap]
rs4877756	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.99[ASN][1000 genomes]
rs4877757	0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[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	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3860901	TLE1	cis	parietal	SCAN
rs3860901	C9orf64	cis	parietal	SCAN
rs3860901	CHFR	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85923600-85960600	Weak transcription	Right Ventricle	heart
2	chr9:85937400-85998000	Weak transcription	Aorta	Aorta
3	chr9:85942600-85970200	Weak transcription	Psoas Muscle	Psoas
4	chr9:85943400-85961600	Weak transcription	Adipose Nuclei	Adipose
5	chr9:85943400-85964400	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:85946200-85963800	Weak transcription	Fetal Brain Female	brain
7	chr9:85950200-85976000	Weak transcription	HepG2	liver
8	chr9:85954800-85960400	Weak transcription	Lung	lung
9	chr9:85955400-85964000	Weak transcription	Ovary	ovary
10	chr9:85956200-85986600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:85958200-85961800	Weak transcription	NHDF-Ad	bronchial
12	chr9:85958200-85980600	Weak transcription	Left Ventricle	heart
13	chr9:85958200-86007600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:85958800-85963800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:85959000-85961000	Weak transcription	Spleen	Spleen
16	chr9:85959000-85963800	Weak transcription	Fetal Heart	heart

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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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