Variant report

Variant	rs11846071
Chromosome Location	chr14:31006665-31006666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10146357	0.94[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap]
rs10147257	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs10149966	0.81[EUR][1000 genomes]
rs1113946	0.83[CEU][hapmap];0.81[MKK][hapmap]
rs1123860	0.94[CEU][hapmap]
rs11624235	0.85[AMR][1000 genomes]
rs11626600	0.80[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11627421	0.94[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap]
rs11628700	0.89[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11846408	0.94[CEU][hapmap]
rs12881161	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12882931	0.94[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap]
rs12888568	0.83[CEU][hapmap]
rs12894186	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17096941	0.94[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs17097023	0.94[CEU][hapmap]
rs17097160	0.83[CEU][hapmap]
rs1840399	0.84[ASN][1000 genomes]
rs2038451	0.82[CEU][hapmap]
rs2057284	0.81[EUR][1000 genomes]
rs2070340	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs2273521	0.94[CEU][hapmap]
rs2273522	0.94[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs229168	0.84[ASN][1000 genomes]
rs229175	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs229215	0.82[AMR][1000 genomes]
rs34935871	0.81[EUR][1000 genomes]
rs35069045	0.94[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap]
rs35389182	0.81[AMR][1000 genomes]
rs3736773	0.83[CEU][hapmap]
rs4430662	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs55725270	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7141624	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7153747	0.85[CHD][hapmap]
rs7156431	0.98[ASN][1000 genomes]
rs761956	0.94[CEU][hapmap]
rs8008094	0.94[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs8013017	0.83[CEU][hapmap]
rs8020220	0.86[AMR][1000 genomes];1.00[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	nsv564169	chr14:30819087-31541494	Strong transcription Genic enhancers ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1036419	chr14:30969616-31224226	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901581	chr14:30978745-31585289	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11846071	SCFD1	cis	parietal	SCAN
rs11846071	SCFD1	cis	cerebellum	SCAN
rs11846071	G2E3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31002400-31020800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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