Variant report

Variant	rs2025404
Chromosome Location	chr13:38318204-38318205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12874536	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1360625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1556541	0.91[MEX][hapmap]
rs1577005	0.81[AMR][1000 genomes]
rs1577006	0.96[EUR][1000 genomes]
rs1577007	0.81[AMR][1000 genomes]
rs763969	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7997030	0.81[AMR][1000 genomes]
rs914862	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9532111	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532112	0.98[EUR][1000 genomes]
rs9532113	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548037	0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548039	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548043	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9576346	0.97[EUR][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	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2025404	RFXAP	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38307600-38330800	Weak transcription	Ovary	ovary
2	chr13:38308200-38328200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr13:38309200-38320600	Weak transcription	NHLF	lung
4	chr13:38309600-38321000	Weak transcription	Osteobl	bone
5	chr13:38310800-38318400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr13:38316000-38318400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:38316000-38320200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:38316000-38321000	Weak transcription	NHDF-Ad	bronchial
9	chr13:38316000-38328200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr13:38316600-38320600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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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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