Variant report

Variant	rs13126929
Chromosome Location	chr4:122075116-122075117
allele	C/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	NFIC	chr4:122075080-122075671	GM12878	blood:	n/a	n/a
2	RUNX3	chr4:122075090-122075724	GM12878	blood:	n/a	chr4:122075369-122075378 chr4:122075369-122075378
3	RUNX3	chr4:122075083-122075646	GM12878	blood:	n/a	chr4:122075369-122075378 chr4:122075369-122075378
4	FOXM1	chr4:122075099-122075657	GM12878	blood:	n/a	n/a
5	NFIC	chr4:122075115-122075666	GM12878	blood:	n/a	n/a
6	ATF2	chr4:122075100-122075725	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TNIP3	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10015340	0.81[EUR][1000 genomes]
rs10446733	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10454795	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10518383	0.85[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11098605	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947841	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13101385	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13102428	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13106084	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13106137	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13107912	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13108214	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13108739	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13109100	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13115256	0.81[EUR][1000 genomes]
rs13116723	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13116936	0.81[EUR][1000 genomes]
rs13118027	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13118818	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13118913	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13123960	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13124511	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13124522	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13128962	0.83[EUR][1000 genomes]
rs13129000	0.83[EUR][1000 genomes]
rs13129293	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13133184	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13133221	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13133584	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138203	0.90[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13143534	0.81[EUR][1000 genomes]
rs13150702	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151913	0.81[EUR][1000 genomes]
rs13152159	0.81[EUR][1000 genomes]
rs13152687	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1511094	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17051320	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17051321	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1858291	0.80[CEU][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2068019	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2136942	0.81[EUR][1000 genomes]
rs2136943	0.81[EUR][1000 genomes]
rs2198315	0.81[EUR][1000 genomes]
rs2218959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28513714	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28530598	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35449703	0.91[ASN][1000 genomes]
rs35971082	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36087391	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3817171	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6534254	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]
rs6811411	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6812399	0.80[EUR][1000 genomes]
rs6814480	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6820363	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821331	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828327	0.88[EUR][1000 genomes]
rs6833114	0.85[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6835790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838000	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6839386	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6839726	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6846458	0.85[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6855628	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6856825	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71629498	0.87[ASN][1000 genomes]
rs7680038	0.81[EUR][1000 genomes]
rs7684168	0.82[EUR][1000 genomes]
rs867883	0.88[EUR][1000 genomes]
rs896621	0.80[EUR][1000 genomes]
rs9307490	0.81[EUR][1000 genomes]
rs998327	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992960	0.81[EUR][1000 genomes]
rs9993163	0.81[EUR][1000 genomes]
rs9998339	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13126929	TNIP3	cis	cerebellum	SCAN
rs13126929	PRDM5	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122073000-122076400	Enhancers	Fetal Thymus	thymus
2	chr4:122073200-122075600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:122073200-122077600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:122073400-122076600	Weak transcription	Osteobl	bone
5	chr4:122073600-122075600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:122073600-122076400	Weak transcription	NHDF-Ad	bronchial
7	chr4:122073600-122076600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:122074000-122077000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:122074600-122076000	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr4:122074600-122076600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr4:122074800-122075400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:122074800-122075600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr4:122074800-122075800	Flanking Active TSS	Dnd41	blood
14	chr4:122074800-122076000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
15	chr4:122074800-122076000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:122074800-122076000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr4:122074800-122076000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr4:122075000-122075200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:122075000-122075200	Enhancers	Small Intestine	intestine
20	chr4:122075000-122075400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr4:122075000-122075400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr4:122075000-122075400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:122075000-122075400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:122075000-122075400	Enhancers	Fetal Lung	lung
25	chr4:122075000-122075600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr4:122075000-122075600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr4:122075000-122075600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:122075000-122075600	Flanking Active TSS	Thymus	Thymus
29	chr4:122075000-122075600	Flanking Active TSS	GM12878-XiMat	blood
30	chr4:122075000-122075800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr4:122075000-122075800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr4:122075000-122076000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr4:122075000-122076000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:122075000-122076000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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