Variant report

Variant	rs2909003
Chromosome Location	chr12:12208769-12208770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12370340	1.00[CHB][hapmap]
rs2448062	0.85[EUR][1000 genomes]
rs2909000	0.86[ASN][1000 genomes]
rs2909001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]
rs2927909	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2927910	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35659587	0.88[EUR][1000 genomes]
rs4315210	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4318056	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4321036	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4331198	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4763760	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9783457	0.86[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2909003	FOXC1	trans	brain	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12199200-12209200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:12200200-12213600	Weak transcription	Right Atrium	heart
3	chr12:12207400-12209000	Enhancers	HepG2	liver
4	chr12:12207800-12208800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:12208200-12210400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr12:12208400-12209200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:12208400-12209200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:12208400-12211400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:12208600-12210400	Enhancers	HUES48 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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