Variant report

Variant	rs11171739
Chromosome Location	chr12:56470625-56470626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56434525..56442579-chr12:56469196..56475242,12	K562	blood:

Variant related genes	Relation type
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 43 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10876864	0.92[ASW][hapmap];0.84[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10876870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1131017	0.91[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1701704	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2271194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292239	0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2456973	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2640562	0.86[ASN][1000 genomes]
rs3741499	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4759229	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs705696	0.87[ASN][1000 genomes]
rs705704	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7297175	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305461	0.81[JPT][hapmap]
rs7312770	0.96[ASN][1000 genomes]
rs772921	0.94[JPT][hapmap]
rs773109	0.82[JPT][hapmap]
rs7971751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs877636	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 1 diabetes	17554300	GWAS catalog

mRNA abundance (count:42)

SNP	Gene	Cis/trans	Tissue	Source
rs11171739	LOC441502	trans	multi-tissue	Pritchard
rs11171739	RPS26	cis	Liver	GTEx
rs11171739	RPS26P40	cis	Liver	GTEx
rs11171739	MYL6B	cis	cerebellum	SCAN
rs11171739	RPS26P6	cis	Liver	GTEx
rs11171739	DNAJC14	cis	parietal	SCAN
rs11171739	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs11171739	SUOX	cis	Thyroid	GTEx
rs11171739	RPS26	cis	multi-tissue	Pritchard
rs11171739	LOC441377	trans	multi-tissue	Pritchard
rs11171739	RPS26P54	cis	Liver	GTEx
rs11171739	RPS26	cis	lymphoblastoid	seeQTL
rs11171739	KRTAP10-1	cis	Liver	GTEx
rs11171739	RPS26	cis	Nerve Tibial	GTEx
rs11171739	MAGEC1	trans	multi-tissue	Pritchard
rs11171739	MADCAM1	trans	multi-tissue	Pritchard
rs11171739	NSMAF	cis	Liver	GTEx
rs11171739	HOXC8	cis	cerebellum	SCAN
rs11171739	RPS26P38	cis	Liver	GTEx
rs11171739	RPS26	cis	brain	seeQTL
rs11171739	ERBB3	cis	parietal	SCAN
rs11171739	SUOX	cis	parietal	SCAN
rs11171739	FLT1	trans	lymphoblastoid	seeQTL
rs11171739	RPS26P28	cis	Liver	GTEx
rs11171739	RPS26P15	cis	Liver	GTEx
rs11171739	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs11171739	RPS26P2	cis	Liver	GTEx
rs11171739	RPS26P31	cis	Liver	GTEx
rs11171739	RPS26	trans	brain	seeQTL
rs11171739	RPS26P10	trans	multi-tissue	Pritchard
rs11171739	RPS26P11	trans	lymphoblastoid	seeQTL
rs11171739	HSS00371222	trans	multi-tissue	Pritchard
rs11171739	RPS26P32	cis	Liver	GTEx
rs11171739	KRTAP10-1	trans	multi-tissue	Pritchard
rs11171739	SUOX	cis	cerebellum	SCAN
rs11171739	RPS26P50	cis	Liver	GTEx
rs11171739	LOC644934	trans	multi-tissue	Pritchard
rs11171739	CCDC4	trans	multi-tissue	Pritchard
rs11171739	FLJ20280	trans	multi-tissue	Pritchard
rs11171739	RPS26P39	cis	Liver	GTEx
rs11171739	SUOX	cis	multi-tissue	Pritchard
rs11171739	TESSP1	cis	Liver	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
2	chr12:56466200-56472400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:56466400-56471800	Weak transcription	Hela-S3	cervix
4	chr12:56466400-56472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:56466600-56472600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:56466600-56472800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:56468000-56472800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:56468200-56472600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:56468600-56472600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:56468800-56471400	Weak transcription	HepG2	liver
11	chr12:56470400-56472600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:56470400-56472600	Weak transcription	NHEK	skin

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