Variant report

Variant	rs11147671
Chromosome Location	chr13:38345195-38345196
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11147667	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11147668	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11147670	0.90[ASW][hapmap];0.94[GIH][hapmap];0.97[MKK][hapmap]
rs11618049	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11620255	0.85[AFR][1000 genomes]
rs12429540	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12430948	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12858218	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12861121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12869016	0.80[ASN][1000 genomes]
rs12874552	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12875518	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12875577	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1333358	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1924301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2025402	0.90[ASW][hapmap];0.87[GIH][hapmap];0.90[MKK][hapmap]
rs34907223	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35989386	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs61955521	0.90[AFR][1000 genomes];0.91[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	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
3	esv2753974	chr13:38341331-38363450	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11147671	RFXAP	cis	cerebellum	SCAN
rs11147671	CD79A	trans	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38341000-38349800	Weak transcription	Osteobl	bone
2	chr13:38342800-38349800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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