Variant report

Variant	rs1336223
Chromosome Location	chr6:163794538-163794539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11751433	0.89[ASN][1000 genomes]
rs11760168	0.94[ASN][1000 genomes]
rs11962088	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs13202116	0.87[ASN][1000 genomes]
rs13202733	0.87[ASN][1000 genomes]
rs13204052	0.87[ASN][1000 genomes]
rs1336224	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414724	0.82[ASN][1000 genomes]
rs1591536	0.82[ASN][1000 genomes]
rs1737319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1737320	0.90[ASN][1000 genomes]
rs1737321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1737324	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1737325	0.88[ASN][1000 genomes]
rs1737326	0.88[ASN][1000 genomes]
rs1737327	0.84[ASN][1000 genomes]
rs1737328	0.83[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1764009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764010	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1764011	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1764012	0.88[ASN][1000 genomes]
rs1764013	0.88[ASN][1000 genomes]
rs1764015	0.82[ASN][1000 genomes]
rs1764019	0.82[ASN][1000 genomes]
rs1764020	0.86[ASN][1000 genomes]
rs2064224	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2064226	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064227	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064230	0.81[ASN][1000 genomes]
rs2744419	0.82[AMR][1000 genomes]
rs2744422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2784871	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2784872	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784875	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857503	0.81[ASN][1000 genomes]
rs3857504	0.83[JPT][hapmap]
rs3904720	0.83[JPT][hapmap]
rs4263561	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4709713	0.92[ASN][1000 genomes]
rs4709714	0.82[ASN][1000 genomes]
rs6455897	0.88[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6908317	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6921172	0.84[ASN][1000 genomes]
rs6927805	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929436	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939218	0.84[JPT][hapmap]
rs718878	0.82[ASN][1000 genomes]
rs718879	0.82[ASN][1000 genomes]
rs9364687	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv970668	chr6:163792636-163802489	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1336223	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163791000-163813000	Weak transcription	Right Atrium	heart
2	chr6:163792400-163796200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:163792400-163796400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:163793800-163794800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr6:163793800-163795200	Enhancers	Spleen	Spleen
6	chr6:163794000-163794600	Bivalent Enhancer	HepG2	liver
7	chr6:163794200-163794600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:163794200-163794600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:163794200-163794600	Enhancers	Left Ventricle	heart
10	chr6:163794400-163794600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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