Variant report

Variant	rs1376117
Chromosome Location	chr4:93476398-93476399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1031319	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516910	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10856893	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10856894	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10856895	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11097340	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097342	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11934648	0.82[ASN][1000 genomes]
rs11935893	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12500504	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12501529	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12504452	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12508312	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12508332	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12508369	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12508403	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12643761	0.80[ASN][1000 genomes]
rs1450500	0.97[ASN][1000 genomes]
rs16996340	0.94[ASN][1000 genomes]
rs17019562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17019608	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17019627	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17019635	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17019639	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17019672	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2012741	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2870639	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34047273	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34191803	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34612832	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs36029067	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4263360	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57113788	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62307820	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310102	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62310103	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62310104	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62310105	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62310106	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62310107	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62310108	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6532376	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6532377	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6829016	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6829672	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6830091	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6832010	0.82[ASN][1000 genomes]
rs6832040	0.82[ASN][1000 genomes]
rs6851143	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6851174	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6851509	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6856270	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6856480	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7661849	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7661958	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7662234	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7662251	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7663643	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7663835	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7667310	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7672511	0.80[ASN][1000 genomes]
rs7685707	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7686323	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7686351	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7686533	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7686627	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7688395	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7688913	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7688929	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7688955	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7689379	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7690138	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7690473	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7691365	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7692235	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695324	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs921354	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9684124	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9685335	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9685970	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948712	chr4:93007985-93740409	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1005500	chr4:93359923-93590452	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv537184	chr4:93359923-93590452	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv879605	chr4:93376231-93740409	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1006957	chr4:93389054-93511561	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv879606	chr4:93391251-93479275	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1013199	chr4:93395509-93511052	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv594869	chr4:93434136-93480717	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv879607	chr4:93434872-93515166	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1014431	chr4:93464326-93618241	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv537185	chr4:93464326-93618241	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1376117	ATOH1	cis	parietal	SCAN
rs1376117	SMARCAD1	cis	cerebellum	SCAN
rs1376117	GRID2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:93457200-93476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:93460000-93476600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr4:93467400-93476400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:93470800-93476400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:93474200-93476600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:93475200-93478000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:93476200-93477200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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