Variant report

Variant	rs6534254
Chromosome Location	chr4:122085994-122085995
allele	A/C
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	STAT3	chr4:122085212-122086042	MCF10A-Er-Src	breast:	n/a	chr4:122086019-122086028 chr4:122085828-122085837 chr4:122085829-122085838 chr4:122086020-122086029
2	FOS	chr4:122085138-122086197	MCF10A-Er-Src	breast:	n/a	chr4:122085830-122085837 chr4:122085829-122085837 chr4:122085829-122085838 chr4:122086020-122086027 chr4:122085567-122085581 chr4:122086019-122086029 chr4:122085827-122085838 chr4:122086020-122086028
3	FOS	chr4:122085315-122086011	HUVEC	blood vessel:	n/a	chr4:122085830-122085837 chr4:122085829-122085837 chr4:122085829-122085838 chr4:122085567-122085581 chr4:122085827-122085838
4	FOS	chr4:122085383-122086062	MCF10A-Er-Src	breast:	n/a	chr4:122085830-122085837 chr4:122085829-122085837 chr4:122085829-122085838 chr4:122086020-122086027 chr4:122085567-122085581 chr4:122086019-122086029 chr4:122085827-122085838 chr4:122086020-122086028
5	STAT3	chr4:122085109-122086091	MCF10A-Er-Src	breast:	n/a	chr4:122086019-122086028 chr4:122085828-122085837 chr4:122085829-122085838 chr4:122086020-122086029
6	STAT3	chr4:122085221-122086216	MCF10A-Er-Src	breast:	n/a	chr4:122086019-122086028 chr4:122085828-122085837 chr4:122085829-122085838 chr4:122086020-122086029
7	FOS	chr4:122085352-122086106	MCF10A-Er-Src	breast:	n/a	chr4:122085830-122085837 chr4:122085829-122085837 chr4:122085829-122085838 chr4:122086020-122086027 chr4:122085567-122085581 chr4:122086019-122086029 chr4:122085827-122085838 chr4:122086020-122086028
8	FOS	chr4:122085264-122086165	MCF10A-Er-Src	breast:	n/a	chr4:122085830-122085837 chr4:122085829-122085837 chr4:122085829-122085838 chr4:122086020-122086027 chr4:122085567-122085581 chr4:122086019-122086029 chr4:122085827-122085838 chr4:122086020-122086028

Variant related genes	Relation type
TNIP3	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10015340	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10446733	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454795	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518383	0.83[GIH][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs11098605	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11947841	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102428	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104663	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13104875	0.81[ASN][1000 genomes]
rs13106084	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106137	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107912	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108214	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13108739	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs13109100	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112923	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13115256	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13116723	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116936	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13118027	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118818	0.82[EUR][1000 genomes]
rs13118913	0.86[EUR][1000 genomes]
rs13123960	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124511	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124522	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126929	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13128962	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13129000	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13129293	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133184	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13133221	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133584	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13137539	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13138203	0.85[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs13143534	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13150702	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13151913	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13152159	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13152687	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511094	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17051320	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051321	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858291	0.80[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2068019	0.86[EUR][1000 genomes]
rs2136942	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2136943	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2198315	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2218959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28513714	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28530598	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35449703	0.97[ASN][1000 genomes]
rs35971082	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36087391	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817171	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6811411	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812399	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6812515	0.84[ASN][1000 genomes]
rs6814480	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820363	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6821331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6828327	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6833114	0.83[GIH][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs6835790	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6838000	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839386	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839726	0.88[EUR][1000 genomes]
rs6846458	0.83[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6855628	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6856825	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71629498	0.94[ASN][1000 genomes]
rs7680038	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7684168	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs867883	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs896621	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9284633	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9307490	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs998327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9992960	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9993163	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9998339	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3386870	chr4:121867625-122208448	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879860	chr4:122030864-122126808	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6534254	TNIP3	cis	cerebellum	SCAN
rs6534254	PRDM5	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122079000-122086400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:122079600-122086400	Weak transcription	Thymus	Thymus
3	chr4:122085000-122086200	Enhancers	NHEK	skin
4	chr4:122085200-122086000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:122085400-122086400	Enhancers	Primary T cells from cord blood	blood
6	chr4:122085600-122086400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:122085600-122089200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr4:122085800-122086200	Enhancers	HUVEC	blood vessel
9	chr4:122085800-122089000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:122085800-122089000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:122085800-122089000	Weak transcription	Monocytes-CD14+_RO01746	blood

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