Variant report

Variant	rs2839775
Chromosome Location	chr12:42114085-42114086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11181110	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181123	0.94[EUR][1000 genomes]
rs11610493	0.86[EUR][1000 genomes]
rs12318357	0.88[EUR][1000 genomes]
rs182293	0.86[EUR][1000 genomes]
rs2060756	0.88[EUR][1000 genomes]
rs287012	0.85[EUR][1000 genomes]
rs287023	0.84[EUR][1000 genomes]
rs287024	0.81[EUR][1000 genomes]
rs383946	0.84[EUR][1000 genomes]
rs395925	0.84[EUR][1000 genomes]
rs397496	0.84[EUR][1000 genomes]
rs414030	0.84[EUR][1000 genomes]
rs438187	0.88[EUR][1000 genomes]
rs4631944	0.88[EUR][1000 genomes]
rs7971920	0.95[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv832386	chr12:42017259-42189476	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899043	chr12:42058138-42313665	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv899044	chr12:42058138-42321161	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2839775	FAF1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42103000-42118800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:42112600-42114400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr12:42113400-42114200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:42113400-42114400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:42113800-42114200	Weak transcription	Brain Germinal Matrix	brain
6	chr12:42113800-42114400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:42113800-42114400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr12:42113800-42114400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr12:42113800-42114400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr12:42114000-42114400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr12:42114000-42114600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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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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