Variant report

Variant	rs11748709
Chromosome Location	chr5:103480474-103480475
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10042762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11745594	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1362697	0.80[ASN][1000 genomes]
rs1420866	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1420867	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1592631	0.82[ASN][1000 genomes]
rs1882562	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1882563	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1882564	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1882565	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1882566	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1882567	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1895020	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1895021	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1922488	0.98[ASN][1000 genomes]
rs1922505	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1922506	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1922508	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1981768	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1981769	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1981770	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1990749	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2542083	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2542084	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2542085	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2542086	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2542087	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2542088	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707404	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707405	0.84[ASN][1000 genomes]
rs2707406	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707407	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707408	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2707409	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2707410	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707411	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707412	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2952550	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2952551	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35090102	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857362	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515272	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4519904	0.87[ASN][1000 genomes]
rs4703287	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4703288	0.84[ASN][1000 genomes]
rs4703289	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6596566	0.87[ASN][1000 genomes]
rs6861405	1.00[ASN][1000 genomes]
rs6866289	1.00[ASN][1000 genomes]
rs6874424	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025859	chr5:102744479-103710290	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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
2	nsv537833	chr5:102744479-103710290	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv882524	chr5:103237745-104019292	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1019939	chr5:103380722-103770101	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537836	chr5:103380722-103770101	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1033278	chr5:103383207-103773361	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv462330	chr5:103406680-103533884	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv599201	chr5:103406680-103533884	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv462333	chr5:103462634-103491763	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv599204	chr5:103462634-103491763	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv508373	chr5:103464035-103487391	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
12	nsv599205	chr5:103478518-103614650	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11748709	FAM174A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:103480200-103480800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:103480400-103483400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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