Variant report

Variant	rs11742241
Chromosome Location	chr5:100028237-100028238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10515269	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10900756	0.81[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11241657	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12153759	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12656404	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12658518	0.82[EUR][1000 genomes]
rs1445170	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1445171	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1445172	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1445173	0.88[EUR][1000 genomes]
rs1963465	0.85[EUR][1000 genomes]
rs2120913	0.81[LWK][hapmap]
rs2590413	0.85[AMR][1000 genomes]
rs2590420	0.89[AMR][1000 genomes]
rs2590421	0.89[AMR][1000 genomes]
rs2590422	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2590423	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2590424	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2725107	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2725110	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs33966109	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34612958	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36038742	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6595380	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6595414	0.85[EUR][1000 genomes]
rs6867428	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6873910	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6874602	0.85[EUR][1000 genomes]
rs6890822	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7701876	0.86[AMR][1000 genomes]
rs7732166	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	nsv882466	chr5:99936090-100029620	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv882467	chr5:99952282-100100157	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv882468	chr5:99959205-100029620	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv882469	chr5:100018392-100082355	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv882470	chr5:100018392-100100157	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11742241	FAM174A	cis	parietal	SCAN
rs11742241	UNQ1912	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100027400-100029400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:100028000-100029600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr5:100028200-100028400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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