Variant report

Variant	rs6460308
Chromosome Location	chr7:66084740-66084741
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: 136 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10215132	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10215516	0.85[EUR][1000 genomes]
rs10229345	0.82[EUR][1000 genomes]
rs10234018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10249404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10252765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[EUR][1000 genomes]
rs10255377	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10263935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10272357	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10272546	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10274773	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10278371	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10278816	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10281080	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10281646	0.81[AMR][1000 genomes]
rs10950044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11028	0.82[YRI][hapmap]
rs1110414	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11765356	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11766262	0.82[EUR][1000 genomes]
rs11768727	0.91[EUR][1000 genomes]
rs11771318	0.81[EUR][1000 genomes]
rs11772264	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11772636	0.92[EUR][1000 genomes]
rs11773829	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532998	0.91[YRI][hapmap]
rs12533585	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12698534	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13224319	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13227951	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1553609	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1553610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[EUR][1000 genomes]
rs17566701	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1860468	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1860470	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1961155	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1968127	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2003301	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2013222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2055682	0.86[EUR][1000 genomes]
rs2077593	0.84[YRI][hapmap]
rs2191268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2244022	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs2286683	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2286684	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2302918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2420824	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2420827	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659889	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2659899	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659906	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659909	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659912	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659915	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2659916	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2707822	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2707827	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2707836	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2707841	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2707845	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707848	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2707849	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2707850	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2707852	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2707853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2707854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[EUR][1000 genomes]
rs2707856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28698552	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28830215	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3069894	0.89[EUR][1000 genomes]
rs34356500	0.88[EUR][1000 genomes]
rs35130766	0.88[EUR][1000 genomes]
rs35526611	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35986979	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3735148	0.90[YRI][hapmap]
rs3764903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778909	0.89[EUR][1000 genomes]
rs3800812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3800820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3800823	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3857686	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3857688	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3898855	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4273746	0.80[EUR][1000 genomes]
rs4279493	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4398788	0.81[AMR][1000 genomes]
rs4717310	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4717319	0.90[EUR][1000 genomes]
rs4718361	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4718403	0.89[EUR][1000 genomes]
rs4718405	0.84[EUR][1000 genomes]
rs56229325	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62465434	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62466793	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62466794	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62467857	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6460296	0.88[YRI][hapmap]
rs6460305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6460309	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6943696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6945019	0.92[YRI][hapmap]
rs6945032	0.91[YRI][hapmap]
rs6947808	0.87[YRI][hapmap]
rs6949912	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6952407	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs6958520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6960778	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6965056	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6979488	0.90[EUR][1000 genomes]
rs71563125	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7357230	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7779971	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7782320	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7783924	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7785213	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7788576	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7789184	0.93[EUR][1000 genomes]
rs7789419	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789768	0.91[YRI][hapmap]
rs7793569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7807930	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7807944	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801190	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs801193	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs801196	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801201	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs801205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801211	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs801216	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs801217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs810400	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9791890	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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
rs6460308	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6460308	RP4-756H11.3	cis	Artery Aorta	GTEx
rs6460308	RP4-756H11.3	cis	Stomach	GTEx
rs6460308	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6460308	RP4-756H11.3	cis	Thyroid	GTEx
rs6460308	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6460308	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6460308	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6460308	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460308	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6460308	RP4-756H11.3	cis	lung	GTEx
rs6460308	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:17 , 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	chr7:66083400-66085000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr7:66083400-66085000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr7:66083400-66085400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr7:66083400-66085400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:66083600-66085200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr7:66083800-66085000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:66084000-66085000	Enhancers	Fetal Stomach	stomach
10	chr7:66084000-66085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:66084200-66084800	Enhancers	K562	blood
12	chr7:66084200-66085000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:66084400-66084800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:66084400-66085000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:66084600-66085000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr7:66084600-66085000	Weak transcription	HepG2	liver
17	chr7:66084600-66085200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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