Variant report

Variant	rs16856409
Chromosome Location	chr1:180699554-180699555
allele	A/G
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:19)

rs_ID	r²[population]
rs10494535	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10914054	0.94[MKK][hapmap]
rs12401315	0.84[ASW][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12401914	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12402575	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap]
rs12403017	0.89[ASN][1000 genomes]
rs12404501	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12408146	0.84[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12408176	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565658	0.83[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs12566450	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs12759582	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs16856361	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap]
rs16856367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16856422	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17302054	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs34451113	0.83[ASN][1000 genomes]
rs4439326	0.84[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74135839	0.89[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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16856409	RGS16	cis	cerebellum	SCAN
rs16856409	FUBP1	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180687000-180700400	Weak transcription	K562	blood
2	chr1:180691400-180701800	Weak transcription	Left Ventricle	heart
3	chr1:180692200-180699800	Weak transcription	Aorta	Aorta
4	chr1:180698000-180704200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:180698400-180700200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:180698800-180703200	Weak transcription	Psoas Muscle	Psoas
7	chr1:180699200-180700600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:180699400-180700200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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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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