Variant report

Variant	rs6812515
Chromosome Location	chr4:122122455-122122456
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:122120724..122123335-chr4:122133956..122135681,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10004221	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10015340	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10446733	0.84[ASN][1000 genomes]
rs10454795	0.84[ASN][1000 genomes]
rs11947841	0.84[ASN][1000 genomes]
rs13101385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13102428	0.84[ASN][1000 genomes]
rs13104663	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13104875	0.97[ASN][1000 genomes]
rs13106084	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13106137	0.84[ASN][1000 genomes]
rs13107912	0.84[ASN][1000 genomes]
rs13109100	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13112923	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13115256	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116723	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13116936	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118027	0.84[ASN][1000 genomes]
rs13123960	0.84[ASN][1000 genomes]
rs13124511	0.84[ASN][1000 genomes]
rs13124522	0.84[ASN][1000 genomes]
rs13125962	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13126929	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs13128962	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129000	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129293	0.84[ASN][1000 genomes]
rs13133184	0.81[ASN][1000 genomes]
rs13133221	0.84[ASN][1000 genomes]
rs13137539	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13143534	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151913	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13152159	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13152687	0.84[ASN][1000 genomes]
rs17051320	0.84[ASN][1000 genomes]
rs17051321	0.84[ASN][1000 genomes]
rs1858291	0.83[GIH][hapmap]
rs2136942	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136943	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198315	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28513714	0.84[ASN][1000 genomes]
rs28530598	0.84[ASN][1000 genomes]
rs35449703	0.81[ASN][1000 genomes]
rs36087391	0.84[ASN][1000 genomes]
rs3817171	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs6534254	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs6811411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6812399	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814480	0.84[ASN][1000 genomes]
rs6821331	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6835790	1.00[CHB][hapmap]
rs6838000	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6839386	0.84[ASN][1000 genomes]
rs6855628	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7680038	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684168	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896621	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284633	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307490	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9992960	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993163	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998339	0.86[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6812515	TNIP3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122120200-122122600	Enhancers	Primary T cells fromperipheralblood	blood
2	chr4:122120200-122122800	Flanking Active TSS	GM12878-XiMat	blood
3	chr4:122120400-122122800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:122120800-122122600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:122121200-122122600	Enhancers	Primary B cells from peripheral blood	blood
6	chr4:122121600-122122600	Enhancers	Liver	Liver
7	chr4:122121600-122122800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:122122200-122122600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr4:122122200-122122600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr4:122122200-122137600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr4:122122400-122123400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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