Variant report

Variant	rs6460290
Chromosome Location	chr7:65809106-65809107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr7:65809070-65809595	A549	lung:	n/a	chr7:65809339-65809350
2	CEBPB	chr7:65809024-65809575	Hela-S3	cervix:	n/a	chr7:65809339-65809350
3	CEBPB	chr7:65809099-65809506	MCF-7	breast:	n/a	chr7:65809339-65809350
4	CEBPB	chr7:65809045-65809595	MCF-7	breast:	n/a	chr7:65809339-65809350
5	NR2F2	chr7:65809101-65809586	MCF-7	breast:	n/a	n/a
6	CEBPD	chr7:65809103-65809500	K562	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-313P	TF binding region

Extended variants
information (count: 144 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1000464	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1002053	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10224872	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10228885	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10240949	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250544	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10255397	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10256544	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10257911	0.91[EUR][1000 genomes]
rs10260426	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10261398	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10263690	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10272149	0.83[EUR][1000 genomes]
rs10276077	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10282433	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10447522	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10807703	0.88[ASN][1000 genomes]
rs10807704	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1083554	0.88[EUR][1000 genomes]
rs10950033	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11760844	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11764589	0.87[EUR][1000 genomes]
rs11765791	0.81[EUR][1000 genomes]
rs11765965	0.83[AMR][1000 genomes]
rs11769079	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11984115	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12531677	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12534500	0.88[EUR][1000 genomes]
rs12537823	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13225672	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13230545	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13309935	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1532571	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1643375	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1695815	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1695820	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1875057	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2036263	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2036264	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2088653	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2088655	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2173570	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2420173	0.84[EUR][1000 genomes]
rs2420174	0.84[EUR][1000 genomes]
rs2420608	0.85[EUR][1000 genomes]
rs28391294	0.82[EUR][1000 genomes]
rs28491091	0.90[EUR][1000 genomes]
rs2901152	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2901155	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2909688	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34913718	0.85[EUR][1000 genomes]
rs3857685	0.81[EUR][1000 genomes]
rs3893216	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3935391	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4078376	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4149461	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4236208	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4587224	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4623294	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718319	0.83[EUR][1000 genomes]
rs4718324	0.86[EUR][1000 genomes]
rs4718328	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4718329	0.87[EUR][1000 genomes]
rs4718330	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4718356	0.80[EUR][1000 genomes]
rs55748098	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs57739047	0.83[EUR][1000 genomes]
rs6460278	0.90[EUR][1000 genomes]
rs6460279	0.90[EUR][1000 genomes]
rs6460282	0.90[EUR][1000 genomes]
rs6460284	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460287	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460291	0.82[AMR][1000 genomes]
rs6460292	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6460293	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6460301	0.82[EUR][1000 genomes]
rs6460302	0.84[EUR][1000 genomes]
rs6460304	0.83[EUR][1000 genomes]
rs6944374	0.90[EUR][1000 genomes]
rs6951503	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6952182	0.90[EUR][1000 genomes]
rs6952473	0.86[EUR][1000 genomes]
rs6958294	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6959268	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960446	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6962717	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6963228	0.85[EUR][1000 genomes]
rs6964437	0.90[EUR][1000 genomes]
rs6967708	0.84[EUR][1000 genomes]
rs6971752	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6974614	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6976714	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6978028	0.86[EUR][1000 genomes]
rs6979452	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6980451	0.83[EUR][1000 genomes]
rs709595	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs709596	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs709597	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71526537	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7778322	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7781880	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7782704	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782806	0.84[EUR][1000 genomes]
rs7783613	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7783779	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778680	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778682	0.82[AMR][1000 genomes]
rs778684	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778685	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs778686	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778689	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7786892	0.81[EUR][1000 genomes]
rs778690	0.86[EUR][1000 genomes]
rs778697	0.86[EUR][1000 genomes]
rs778702	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778703	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs778705	0.87[EUR][1000 genomes]
rs778707	0.87[EUR][1000 genomes]
rs778711	0.87[EUR][1000 genomes]
rs778715	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778716	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778719	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778720	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778723	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs778724	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778726	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs778728	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs778734	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778735	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs778736	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7787482	0.86[EUR][1000 genomes]
rs7789615	0.84[EUR][1000 genomes]
rs7794930	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7796162	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7798630	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs809025	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs880166	0.93[EUR][1000 genomes]
rs937495	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs949930	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9969301	0.81[AFR][1000 genomes];0.82[AMR][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	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs6460290	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6460290	RP4-756H11.3	cis	Artery Aorta	GTEx
rs6460290	LINC00174	cis	Thyroid	GTEx
rs6460290	RP4-756H11.3	cis	Thyroid	GTEx
rs6460290	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6460290	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs6460290	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6460290	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6460290	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6460290	GS1-124K5.2	cis	Whole Blood	GTEx
rs6460290	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460290	RP4-756H11.3	cis	lung	GTEx
rs6460290	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6460290	GS1-124K5.11	cis	Thyroid	GTEx
rs6460290	GS1-124K5.4	cis	Stomach	GTEx
rs6460290	GTF2IRD1P1	cis	Thyroid	GTEx
rs6460290	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6460290	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6460290	RNU6-96P	cis	Thyroid	GTEx
rs6460290	RP4-756H11.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65796800-65809200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr7:65797200-65811600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:65800800-65812200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:65800800-65813600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:65805200-65843600	Weak transcription	Aorta	Aorta
6	chr7:65807800-65814400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:65808400-65809600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:65809000-65809400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:65809000-65809400	Enhancers	Osteobl	bone
10	chr7:65809000-65809600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:65809000-65809600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:65809000-65809600	Enhancers	Liver	Liver
13	chr7:65809000-65809600	Enhancers	HMEC	breast
14	chr7:65809000-65809800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:65809000-65809800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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