Variant report

Variant	rs2420820
Chromosome Location	chr7:66091907-66091908
allele	C/T
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	FOS	chr7:66091479-66091950	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr7:66091656-66092336	HepG2	liver:	n/a	n/a
3	MAX	chr7:66091719-66091919	Hela-S3	cervix:	n/a	n/a
4	SMC3	chr7:66091575-66091938	HepG2	liver:	n/a	n/a
5	GATA2	chr7:66091819-66092663	SH-SY5Y	brain:	n/a	n/a
6	TEAD4	chr7:66091527-66092015	HepG2	liver:	n/a	n/a
7	CEBPB	chr7:66091533-66092524	IMR90	lung:	n/a	chr7:66091783-66091794
8	CEBPB	chr7:66091582-66091967	Hela-S3	cervix:	n/a	chr7:66091783-66091794
9	EP300	chr7:66091491-66096076	SK-N-SH	brain:	n/a	chr7:66093761-66093770 chr7:66094701-66094715 chr7:66093402-66093418 chr7:66094696-66094710 chr7:66093421-66093437
10	TCF7L2	chr7:66091878-66092540	HEK293	kidney:	n/a	n/a
11	CEBPB	chr7:66091637-66091967	HepG2	liver:	n/a	chr7:66091783-66091794
12	ARID3A	chr7:66091651-66092304	HepG2	liver:	n/a	n/a
13	TBP	chr7:66091734-66092509	HepG2	liver:	n/a	n/a
14	STAT3	chr7:66091630-66091936	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr7:66091460-66091935	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr7:66091595-66091967	HepG2	liver:	n/a	chr7:66091783-66091794
17	POLR2A	chr7:66091849-66094789	IMR90	lung:	n/a	n/a
18	MXI1	chr7:66091233-66095157	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:66065925..66067738-chr7:66091765..66093864,2	MCF-7	breast:
2	chr7:66091898..66097382-chr7:66117985..66122507,10	K562	blood:
3	chr7:66081713..66084655-chr7:66091720..66093835,2	K562	blood:
4	chr7:66091844..66094640-chr7:66118336..66122170,5	MCF-7	breast:

Variant related genes	Relation type
KCTD7	TF binding region
ENSG00000226824	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs1016265	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10233806	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10244498	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10274883	0.91[AFR][1000 genomes]
rs10278014	0.81[AFR][1000 genomes]
rs10950049	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11761542	0.81[AFR][1000 genomes]
rs11772819	0.84[AFR][1000 genomes]
rs12333370	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12532998	0.80[EUR][1000 genomes]
rs12533997	0.80[EUR][1000 genomes]
rs12535036	0.80[EUR][1000 genomes]
rs12673810	0.80[EUR][1000 genomes]
rs12698520	0.80[EUR][1000 genomes]
rs12698523	0.80[EUR][1000 genomes]
rs12698532	0.81[EUR][1000 genomes]
rs13226966	0.84[AFR][1000 genomes]
rs13240501	0.81[AFR][1000 genomes]
rs13242290	0.87[AFR][1000 genomes]
rs13308803	0.85[AFR][1000 genomes]
rs13309022	0.80[EUR][1000 genomes]
rs1363055	0.80[EUR][1000 genomes]
rs1544549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1833495	0.80[EUR][1000 genomes]
rs1860469	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1860472	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1962050	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2003300	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013908	0.90[AFR][1000 genomes]
rs2024192	0.83[AFR][1000 genomes]
rs2042133	0.81[EUR][1000 genomes]
rs2109297	0.91[AFR][1000 genomes]
rs2161065	0.81[EUR][1000 genomes]
rs2420599	0.81[EUR][1000 genomes]
rs2659890	0.82[AFR][1000 genomes]
rs2659891	0.86[AFR][1000 genomes]
rs2659892	0.85[AFR][1000 genomes]
rs2659893	0.85[AFR][1000 genomes]
rs2659894	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659895	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659897	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2659898	0.85[AFR][1000 genomes]
rs2659900	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659901	0.87[AFR][1000 genomes]
rs2659904	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659907	0.85[AFR][1000 genomes]
rs2659908	0.85[AFR][1000 genomes]
rs2659914	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2707824	0.85[AFR][1000 genomes]
rs2707837	0.87[AFR][1000 genomes]
rs2707839	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2707847	0.85[AFR][1000 genomes]
rs28480509	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34406470	0.80[EUR][1000 genomes]
rs35149210	0.81[EUR][1000 genomes]
rs3735148	0.80[EUR][1000 genomes]
rs3846973	0.87[AFR][1000 genomes]
rs3857687	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3926380	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4506088	0.85[AFR][1000 genomes]
rs4610622	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4717299	0.80[EUR][1000 genomes]
rs4717315	0.83[AFR][1000 genomes]
rs4718357	0.81[EUR][1000 genomes]
rs4718377	0.81[AFR][1000 genomes]
rs4718383	0.92[AFR][1000 genomes]
rs58347342	0.83[AFR][1000 genomes]
rs6460300	0.80[EUR][1000 genomes]
rs66981195	0.90[AFR][1000 genomes]
rs6945019	0.80[EUR][1000 genomes]
rs6945032	0.80[EUR][1000 genomes]
rs6951302	0.92[AFR][1000 genomes]
rs6955837	0.83[AFR][1000 genomes]
rs6957199	0.83[EUR][1000 genomes]
rs6958200	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6958271	0.82[EUR][1000 genomes]
rs6958277	0.82[EUR][1000 genomes]
rs6961155	0.80[EUR][1000 genomes]
rs6969679	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6970030	0.81[EUR][1000 genomes]
rs6970357	0.80[EUR][1000 genomes]
rs6970860	0.83[EUR][1000 genomes]
rs6971059	0.82[AFR][1000 genomes]
rs6973249	0.81[AMR][1000 genomes]
rs6975044	0.81[AFR][1000 genomes]
rs6978178	0.91[AFR][1000 genomes]
rs721717	0.92[AFR][1000 genomes]
rs7384021	0.81[AFR][1000 genomes]
rs7781061	0.80[EUR][1000 genomes]
rs7782587	0.82[AFR][1000 genomes]
rs7789768	0.80[EUR][1000 genomes]
rs7792762	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7800620	0.84[AFR][1000 genomes]
rs7808013	0.84[AFR][1000 genomes]
rs881285	0.88[AFR][1000 genomes]
rs9691480	0.80[EUR][1000 genomes]
rs974239	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9791712	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9791713	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2420820	RP4-756H11.3	cis	Thyroid	GTEx
rs2420820	RP4-756H11.3	cis	lung	GTEx
rs2420820	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2420820	GS1-124K5.4	cis	Artery Aorta	GTEx
rs2420820	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2420820	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2420820	GS1-124K5.4	cis	Stomach	GTEx
rs2420820	GS1-124K5.4	cis	Whole Blood	GTEx
rs2420820	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2420820	RP4-756H11.3	cis	Artery Aorta	GTEx
rs2420820	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs2420820	RNU6-96P	cis	Thyroid	GTEx
rs2420820	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2420820	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs2420820	GS1-124K5.11	cis	Thyroid	GTEx
rs2420820	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2420820	GTF2IRD1P1	cis	Thyroid	GTEx
rs2420820	RP4-756H11.3	cis	Artery Tibial	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66086800-66092800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:66087600-66092200	Weak transcription	K562	blood
3	chr7:66087600-66092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:66089800-66092800	Enhancers	Placenta	Placenta
5	chr7:66090200-66092800	Weak transcription	Stomach Mucosa	stomach
6	chr7:66090400-66092200	Enhancers	NHDF-Ad	bronchial
7	chr7:66090400-66092800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:66090600-66092200	Enhancers	Colon Smooth Muscle	Colon
9	chr7:66090600-66093000	Enhancers	NHLF	lung
10	chr7:66090800-66092800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:66091200-66092000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:66091200-66092400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:66091400-66092000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:66091400-66092000	Enhancers	Stomach Smooth Muscle	stomach
15	chr7:66091400-66092400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:66091400-66092400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:66091400-66092800	Enhancers	Osteobl	bone
18	chr7:66091400-66093000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:66091600-66092400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr7:66091600-66092800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:66091800-66092000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:66091800-66092200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:66091800-66092200	Enhancers	Rectal Smooth Muscle	rectum
24	chr7:66091800-66092600	Flanking Active TSS	HepG2	liver
25	chr7:66091800-66092600	Enhancers	NHEK	skin
26	chr7:66091800-66092800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:66091800-66092800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:66091800-66092800	Enhancers	Fetal Stomach	stomach
29	chr7:66091800-66093000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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