Variant report

Variant	rs35123877
Chromosome Location	chr9:100159784-100159785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr9:100159326-100159972	GM12878	blood:	n/a	n/a
2	EBF1	chr9:100159455-100159921	GM12878	blood:	n/a	n/a
3	STAT5A	chr9:100159396-100159857	GM12878	blood:	n/a	n/a
4	BCL11A	chr9:100159468-100159859	GM12878	blood:	n/a	n/a
5	PAX5	chr9:100159586-100159812	GM12878	blood:	n/a	n/a
6	RUNX3	chr9:100159377-100159972	GM12878	blood:	n/a	n/a
7	FOXM1	chr9:100159426-100159949	GM12878	blood:	n/a	n/a
8	BATF	chr9:100159459-100159895	GM12878	blood:	n/a	n/a
9	IKZF1	chr9:100159322-100159925	GM12878	blood:	n/a	n/a
10	PAX5	chr9:100159526-100159795	GM12878	blood:	n/a	n/a
11	MEF2A	chr9:100159466-100159880	GM12878	blood:	n/a	chr9:100159613-100159634 chr9:100159614-100159630 chr9:100159616-100159627 chr9:100159615-100159630 chr9:100159617-100159628
12	PAX5	chr9:100159442-100160000	GM12878	blood:	n/a	n/a
13	EP300	chr9:100159535-100159896	GM12878	blood:	n/a	n/a
14	FOXM1	chr9:100159458-100159929	GM12878	blood:	n/a	n/a
15	EBF1	chr9:100159440-100160000	GM12878	blood:	n/a	n/a
16	NFIC	chr9:100159481-100159965	GM12878	blood:	n/a	n/a
17	IRF4	chr9:100159470-100159954	GM12878	blood:	n/a	n/a
18	MEF2A	chr9:100159462-100159840	GM12878	blood:	n/a	chr9:100159613-100159634 chr9:100159614-100159630 chr9:100159616-100159627 chr9:100159615-100159630 chr9:100159617-100159628
19	BCL11A	chr9:100159538-100159872	GM12878	blood:	n/a	n/a
20	BATF	chr9:100159456-100159960	GM12878	blood:	n/a	n/a
21	PAX5	chr9:100159539-100159902	GM12878	blood:	n/a	n/a
22	ATF2	chr9:100159366-100159963	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr9:100159545-100159824	GM12878	blood:	n/a	n/a
24	NFIC	chr9:100159385-100160009	GM12878	blood:	n/a	n/a
25	POLR2A	chr9:100159419-100159967	GM12892	blood:	n/a	n/a
26	SP1	chr9:100159489-100159867	GM12878	blood:	n/a	n/a
27	EBF1	chr9:100159435-100159843	GM12878	blood:	n/a	n/a
28	MTA3	chr9:100159284-100159944	GM12878	blood:	n/a	n/a
29	IRF4	chr9:100159453-100159960	GM12878	blood:	n/a	n/a
30	ATF2	chr9:100159452-100159921	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:100159780-100159830	SKMC	muscle:	n/a
2	chr9:100159780-100159830	AG09309	skin:	n/a
3	chr9:100159780-100159830	HCM	heart:	n/a
4	chr9:100159780-100159830	MCF-7	breast:	n/a
5	chr9:100159780-100159830	HUVEC	blood vessel:	n/a
6	chr9:100159780-100159830	SK-N-SH	brain:	n/a
7	chr9:100159780-100159830	CMK	blood:	n/a
8	chr9:100159780-100159830	BE2_C	brain:	n/a
9	chr9:100159780-100159830	Hepatocyte	liver:	n/a
10	chr9:100159780-100159830	K562	blood:	n/a
11	chr9:100159780-100159830	Jurkat	blood:	n/a
12	chr9:100159780-100159830	RPTEC	kidney:	n/a
13	chr9:100159780-100159830	A549	lung:	n/a
14	chr9:100159780-100159830	NB4	blood:	n/a
15	chr9:100159780-100159830	GM19239	blood:	n/a
16	chr9:100159780-100159830	HCT-116	colon:	n/a
17	chr9:100159780-100159830	IMR90	lung:	fetal
18	chr9:100159780-100159830	HEEpiC	esophagus:	n/a
19	chr9:100159780-100159830	GM12878	blood:	n/a
20	chr9:100159780-100159830	NT2-D1	testis:	n/a
21	chr9:100159780-100159830	GM06990	blood:	n/a
22	chr9:100159780-100159830	AG10803	skin:	n/a
23	chr9:100159780-100159830	ovcar-3	ovarian:	n/a
24	chr9:100159780-100159830	PANC-1	pancreas:	n/a
25	chr9:100159780-100159830	T-47D	breast:	n/a
26	chr9:100159780-100159830	HRPEpiC	eye:	n/a
27	chr9:100159780-100159830	AG09319	gingival:	n/a
28	chr9:100159780-100159830	HNPCEpiC	eye:	n/a
29	chr9:100159780-100159830	Hela-S3	cervix:	n/a
30	chr9:100159780-100159830	AoSMC	blood vessel:	n/a
31	chr9:100159780-100159830	Caco-2	colon:	n/a
32	chr9:100159780-100159830	HRE	kidney:	n/a
33	chr9:100159780-100159830	HCF	heart:	n/a
34	chr9:100159780-100159830	H1-hESC	embryonic stem cell:	embryo
35	chr9:100159780-100159830	AG04450	lung:	fetal
36	chr9:100159780-100159830	SK-N-SH_RA	brain:	n/a
37	chr9:100159780-100159830	HRCEpiC	kidney:	n/a
38	chr9:100159780-100159830	HIPEpiC	eye:	n/a
39	chr9:100159780-100159830	SK-N-MC	brain:	n/a
40	chr9:100159780-100159830	PrEC	prostate:	n/a
41	chr9:100159780-100159830	ProgFib	skin:	n/a
42	chr9:100159780-100159830	GM12891	blood:	n/a
43	chr9:100159780-100159830	SAEC	small airway:	n/a
44	chr9:100159780-100159830	GM12892	blood:	n/a
45	chr9:100159780-100159830	LNCaP	prostate:	n/a
46	chr9:100159780-100159830	PFSK-1	brain:	n/a
47	chr9:100159780-100159830	ECC-1	luminal epithelium:	n/a
48	chr9:100159780-100159830	HPAEpiC	pulmonary alveolar:	n/a
49	chr9:100159780-100159830	BJ	skin:	n/a
50	chr9:100159780-100159830	HL-60	blood:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100158859..100160754-chr9:100392262..100394128,2	K562	blood:
2	chr9:100158999..100160647-chr9:100162275..100163910,2	MCF-7	breast:
3	chr9:100149625..100153516-chr9:100159731..100163036,3	MCF-7	breast:
4	chr9:100150440..100152091-chr9:100159690..100161456,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228957	TF binding region
ENSG00000228957	CpG island

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1048451	0.88[EUR][1000 genomes]
rs10817384	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10817491	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10817504	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10981444	0.84[EUR][1000 genomes]
rs10981460	0.87[EUR][1000 genomes]
rs10981688	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981701	0.85[AMR][1000 genomes]
rs10981784	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981800	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981801	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1123379	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11581	0.91[EUR][1000 genomes]
rs12115447	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12115448	0.94[EUR][1000 genomes]
rs12377538	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12378350	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12550923	0.83[EUR][1000 genomes]
rs12551740	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12551818	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12552101	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12552659	0.86[EUR][1000 genomes]
rs12553155	0.86[EUR][1000 genomes]
rs12553213	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12553259	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12554363	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12555277	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13285567	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13286510	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13289813	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13292715	0.83[EUR][1000 genomes]
rs13300328	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13301045	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13301965	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1531440	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1564048	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1564050	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16919506	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16919656	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16919661	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16919671	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16919675	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2045729	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2045730	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2045731	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2279113	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290933	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2306090	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2306092	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2306094	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2401384	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34135027	0.87[EUR][1000 genomes]
rs34183765	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34355647	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34476799	0.83[EUR][1000 genomes]
rs34564795	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34609282	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34616426	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34754033	0.86[EUR][1000 genomes]
rs34870571	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34905303	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34954690	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35066943	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35534888	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35623544	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35737497	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35778461	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35778718	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35788892	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747490	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747491	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747492	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747495	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3747498	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747499	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747504	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747506	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3747507	0.90[EUR][1000 genomes]
rs3747510	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747511	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3827484	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3827485	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3994560	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41316960	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742686	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4742688	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743070	0.83[EUR][1000 genomes]
rs4743073	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743082	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743083	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743085	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743086	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62557460	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62557461	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62557462	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62557463	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7038496	0.89[EUR][1000 genomes]
rs7041222	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73565808	0.91[EUR][1000 genomes]
rs7874652	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs898869	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs898870	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9696058	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35123877	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100149600-100161400	Weak transcription	Right Atrium	heart
2	chr9:100157400-100161800	Weak transcription	Thymus	Thymus
3	chr9:100157800-100162000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:100159000-100160400	Weak transcription	HepG2	liver
5	chr9:100159000-100160600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:100159000-100161400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:100159200-100161600	Enhancers	GM12878-XiMat	blood

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