Variant report

Variant	rs6042548
Chromosome Location	chr20:14125227-14125228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11087071	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11696504	1.00[ASN][1000 genomes]
rs11696983	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs11697008	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11697554	1.00[ASN][1000 genomes]
rs11697708	1.00[ASN][1000 genomes]
rs11698906	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap]
rs11699040	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11699117	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12106104	1.00[JPT][hapmap]
rs12106261	1.00[JPT][hapmap]
rs12373859	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1406923	1.00[ASN][1000 genomes]
rs1555412	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1810689	1.00[ASN][1000 genomes]
rs1980701	1.00[ASN][1000 genomes]
rs2038674	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204610	1.00[ASN][1000 genomes]
rs2145561	1.00[ASN][1000 genomes]
rs2209017	1.00[JPT][hapmap]
rs2209018	1.00[ASN][1000 genomes]
rs2209019	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2327818	1.00[JPT][hapmap]
rs2327819	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3940133	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4120825	1.00[JPT][hapmap]
rs4380310	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4814288	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4814289	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4814290	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs59177302	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59461685	1.00[ASN][1000 genomes]
rs6033884	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6033888	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033897	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6042525	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042530	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6042541	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs6042552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042553	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6042581	1.00[ASN][1000 genomes]
rs6074697	1.00[JPT][hapmap]
rs6079309	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6079331	1.00[ASN][1000 genomes]
rs6079346	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6079350	1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs6079353	1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs6105221	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105227	1.00[JPT][hapmap]
rs6110194	1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs7260702	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7261715	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7261965	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7264001	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7273854	1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[YRI][hapmap]
rs73255018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73255080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73264804	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73269439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73900790	1.00[ASN][1000 genomes]
rs8118198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8120693	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8122275	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs8125466	1.00[ASN][1000 genomes]
rs9753755	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979409	1.00[ASN][1000 genomes]
rs979410	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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	17 gene(s)	inside rSNPs	diseases
2	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv585438	chr20:14054163-14171905	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1058887	chr20:14080114-14173534	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv532514	chr20:14097780-14288315	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6042548	LRTM1	trans	brain	seeQTL
rs6042548	SLC5A7	trans	brain	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14123200-14125400	Weak transcription	Gastric	stomach
2	chr20:14123200-14129600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:14123600-14126400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:14123800-14125600	Enhancers	Fetal Intestine Small	intestine
5	chr20:14124200-14125600	Enhancers	Fetal Intestine Large	intestine
6	chr20:14124400-14128400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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