Variant report

Variant	rs56404130
Chromosome Location	chr6:107124848-107124849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1026619	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10457147	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153019	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11752776	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11759803	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11968474	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11968502	0.81[EUR][1000 genomes]
rs12212676	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12214412	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12216505	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13200233	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13202677	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13207581	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1986498	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2169463	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3101493	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3101496	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3101499	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3104038	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3104046	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121434	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121435	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121436	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121437	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121438	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121439	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121440	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121441	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121442	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121444	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121445	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3121448	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3121449	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3127658	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4640924	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2608808	chr6:107123698-107125197	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv989863	chr6:107123802-107124897	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
4	esv3351750	chr6:107123809-107125757	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2180999	chr6:107124346-107125030	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
6	esv3442652	chr6:107124413-107124935	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
7	esv3473153	chr6:107124420-107124908	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
8	esv3511849	chr6:107124431-107124937	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
9	esv3511851	chr6:107124444-107124886	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
10	esv3511850	chr6:107124446-107124866	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv3473154	chr6:107124452-107124899	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
12	esv3473155	chr6:107124461-107124893	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
13	esv3473152	chr6:107124466-107124856	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
14	esv3511848	chr6:107124467-107124888	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
15	esv3511847	chr6:107124476-107124879	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
16	esv3511853	chr6:107124533-107124849	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs56404130	QRSL1	cis	Thyroid	GTEx
rs56404130	QRSL1	cis	Skin Sun Exposed Lower leg	GTEx
rs56404130	QRSL1	Cis_1M	lymphoblastoid	RTeQTL
rs56404130	QRSL1	cis	multi-tissue	Pritchard
rs56404130	QRSL1	cis	Nerve Tibial	GTEx
rs56404130	QRSL1	cis	Esophagus Muscularis	GTEx
rs56404130	QRSL1	cis	Adipose Subcutaneous	GTEx
rs56404130	QRSL1	cis	lung	GTEx
rs56404130	QRSL1	cis	Artery Tibial	GTEx
rs56404130	QRSL1	cis	Muscle Skeletal	GTEx
rs56404130	QRSL1	cis	Heart Left Ventricle	GTEx
rs56404130	QRSL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:107078600-107125200	Weak transcription	Stomach Mucosa	stomach
2	chr6:107106600-107126200	Weak transcription	Psoas Muscle	Psoas
3	chr6:107114000-107125400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:107116800-107125000	Weak transcription	Primary B cells from cord blood	blood
5	chr6:107117600-107130800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:107121000-107125200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:107121000-107125200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:107121200-107125400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:107124800-107126200	Enhancers	Primary B cells from peripheral blood	blood

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