Variant report

Variant	rs6460309
Chromosome Location	chr7:66085153-66085154
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	chr7:66083135..66085201-chr7:66118742..66121004,2	K562	blood:

Variant related genes	Relation type
ENSG00000226824	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10215132	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10234018	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10249404	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10252765	0.82[EUR][1000 genomes]
rs10255377	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10263935	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10272357	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10272546	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10274773	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10278371	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10278816	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10281080	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950044	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1110414	0.81[EUR][1000 genomes]
rs11765356	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11766262	0.82[EUR][1000 genomes]
rs11768727	0.80[EUR][1000 genomes]
rs11771318	0.81[EUR][1000 genomes]
rs11772264	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11772636	0.81[EUR][1000 genomes]
rs11773829	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12533585	0.83[ASN][1000 genomes]
rs12698534	0.83[ASN][1000 genomes]
rs13224319	0.87[ASN][1000 genomes]
rs13227951	0.80[EUR][1000 genomes]
rs1553609	0.82[EUR][1000 genomes]
rs1553610	0.81[EUR][1000 genomes]
rs1860468	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1860470	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1961155	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1968127	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2003301	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2013222	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2191268	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2286683	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2286684	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2302918	0.85[ASN][1000 genomes]
rs2420824	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2420827	0.81[ASN][1000 genomes]
rs2659889	0.81[EUR][1000 genomes]
rs2659906	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659909	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659912	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659915	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2659916	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2707822	0.82[EUR][1000 genomes]
rs2707827	0.81[EUR][1000 genomes]
rs2707836	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707841	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707845	0.81[EUR][1000 genomes]
rs2707848	0.82[AMR][1000 genomes]
rs2707849	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707850	0.82[EUR][1000 genomes]
rs2707853	0.82[EUR][1000 genomes]
rs2707856	0.82[EUR][1000 genomes]
rs28698552	0.85[ASN][1000 genomes]
rs28830215	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35526611	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35986979	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764903	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3800812	0.82[EUR][1000 genomes]
rs3800820	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3857686	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857688	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3898855	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4279493	0.82[EUR][1000 genomes]
rs4717310	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56229325	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62465434	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62466793	0.81[EUR][1000 genomes]
rs62466794	0.82[EUR][1000 genomes]
rs62467857	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460305	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460308	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6943696	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6949912	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6958520	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6960778	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6965056	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71563125	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7357230	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7779971	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7783924	0.81[EUR][1000 genomes]
rs7785213	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7788576	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7789184	0.82[EUR][1000 genomes]
rs7789419	0.81[ASN][1000 genomes]
rs7793569	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7807930	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7807944	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs801190	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801193	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801196	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs801205	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs801211	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs801216	0.87[ASN][1000 genomes]
rs801217	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs810400	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9791890	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6460309	RP4-756H11.3	cis	Thyroid	GTEx
rs6460309	RP4-756H11.3	cis	Artery Aorta	GTEx
rs6460309	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6460309	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6460309	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6460309	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6460309	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6460309	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460309	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6460309	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6460309	RP4-756H11.3	cis	lung	GTEx
rs6460309	GS1-124K5.4	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66083200-66085200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr7:66083200-66085600	Enhancers	Placenta	Placenta
3	chr7:66083400-66085400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr7:66083400-66085400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr7:66083600-66085200	Enhancers	H1 Cell Line	embryonic stem cell
6	chr7:66084000-66085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:66084600-66085200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr7:66084800-66087200	Weak transcription	K562	blood
9	chr7:66085000-66085200	Enhancers	HepG2	liver
10	chr7:66085000-66090800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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