Variant report

Variant	rs10489277
Chromosome Location	chr1:172800805-172800806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10912479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058539	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12120752	0.89[AMR][1000 genomes]
rs12125542	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12142778	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143438	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12144816	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12145987	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17299020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17299078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916281	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704843	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs724901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv947552	chr1:172794244-172807477	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10489277	C1orf129	cis	cerebellum	SCAN
rs10489277	SNORD79	cis	cerebellum	SCAN
rs10489277	MPZL1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172791200-172806200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:172796000-172806200	Weak transcription	HMEC	breast
3	chr1:172796000-172813800	Weak transcription	Small Intestine	intestine
4	chr1:172797400-172801200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:172797600-172801200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:172797600-172804200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:172797800-172801200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:172797800-172803600	Enhancers	Dnd41	blood
9	chr1:172797800-172807000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:172797800-172807000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:172798200-172806600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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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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