Variant report

Variant	rs12599310
Chromosome Location	chr16:52301178-52301179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10521261	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080489	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs1080490	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs12325489	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12930272	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs12930844	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1362376	0.89[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34214423	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34296884	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826196	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67253370	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67505663	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67753568	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72794118	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492248	chr16:51681902-52456082	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv34024	chr16:51878565-52316530	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1066719	chr16:52294981-53141905	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:52297600-52302000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr16:52297600-52302000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr16:52297800-52302200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr16:52297800-52302200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr16:52298000-52301800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr16:52298200-52301400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:52298200-52301600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr16:52299400-52302000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr16:52299600-52302000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr16:52300000-52302000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr16:52300200-52301800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr16:52300200-52301800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr16:52300200-52304400	Weak transcription	Fetal Brain Male	brain
14	chr16:52300400-52302000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr16:52300800-52305000	Weak transcription	Brain Germinal Matrix	brain
16	chr16:52301000-52301400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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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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