Variant report

Variant	rs10981931
Chromosome Location	chr9:100159765-100159766
allele	A/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	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	SRF	chr9:100159562-100159782	GM12878	blood:	n/a	n/a
21	BATF	chr9:100159456-100159960	GM12878	blood:	n/a	n/a
22	PAX5	chr9:100159539-100159902	GM12878	blood:	n/a	n/a
23	ATF2	chr9:100159366-100159963	GM12878	blood:	n/a	n/a
24	TBL1XR1	chr9:100159545-100159824	GM12878	blood:	n/a	n/a
25	NFIC	chr9:100159385-100160009	GM12878	blood:	n/a	n/a
26	POLR2A	chr9:100159419-100159967	GM12892	blood:	n/a	n/a
27	SP1	chr9:100159489-100159867	GM12878	blood:	n/a	n/a
28	EBF1	chr9:100159435-100159843	GM12878	blood:	n/a	n/a
29	MTA3	chr9:100159284-100159944	GM12878	blood:	n/a	n/a
30	IRF4	chr9:100159453-100159960	GM12878	blood:	n/a	n/a
31	ATF2	chr9:100159452-100159921	GM12878	blood:	n/a	n/a

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:

Variant related genes	Relation type
ENSG00000228957	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10122063	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10125198	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1020884	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1020885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1037948	0.89[EUR][1000 genomes]
rs1037950	0.95[EUR][1000 genomes]
rs1037951	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10435868	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10448274	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10759527	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs10759624	0.88[EUR][1000 genomes]
rs10759657	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817273	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs10817286	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs10817487	0.90[EUR][1000 genomes]
rs10981367	0.85[JPT][hapmap]
rs10981460	0.85[JPT][hapmap]
rs10981890	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs10981919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12377538	0.85[JPT][hapmap]
rs12550923	0.85[JPT][hapmap]
rs12551740	0.85[JPT][hapmap]
rs13287082	0.85[JPT][hapmap]
rs13289134	0.85[JPT][hapmap]
rs1531440	0.85[JPT][hapmap]
rs1542506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1947717	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2045729	0.85[JPT][hapmap]
rs2169456	0.96[CEU][hapmap]
rs2242187	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2279114	0.93[EUR][1000 genomes]
rs2290933	0.85[JPT][hapmap]
rs2306094	0.85[JPT][hapmap]
rs2306097	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs3747489	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3747493	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3747495	0.85[JPT][hapmap]
rs3747496	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs3747498	0.85[JPT][hapmap]
rs3747499	0.85[JPT][hapmap]
rs3747504	0.85[JPT][hapmap]
rs3747506	0.85[JPT][hapmap]
rs3802471	0.91[EUR][1000 genomes]
rs3994560	0.85[JPT][hapmap]
rs4237189	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4313271	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4366181	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4523385	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4554595	0.89[EUR][1000 genomes]
rs4742685	0.87[EUR][1000 genomes]
rs4742689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743070	0.85[JPT][hapmap]
rs4743073	0.85[JPT][hapmap]
rs4743076	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4743077	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4743084	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4743087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4743088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478095	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6478131	0.93[EUR][1000 genomes]
rs7038496	0.80[JPT][hapmap]
rs7869536	0.93[EUR][1000 genomes]
rs9696167	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10981931	RP11-520B13.4	cis	Thyroid	GTEx
rs10981931	ANKRD18CP	cis	Thyroid	GTEx
rs10981931	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs10981931	CCDC180	cis	Artery Tibial	GTEx
rs10981931	RP11-498P14.5	cis	lung	GTEx
rs10981931	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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