Variant report

Variant	rs4712882
Chromosome Location	chr6:25043910-25043911
allele	A/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	PML	chr6:25042170-25043982	GM12878	blood:	n/a	n/a
2	ZNF143	chr6:25043802-25044042	GM12878	blood:	n/a	n/a
3	RELA	chr6:25043278-25044182	GM18505	blood:	n/a	n/a
4	RELA	chr6:25042155-25043993	GM18951	blood:	n/a	n/a
5	NFIC	chr6:25041052-25044467	GM12878	blood:	n/a	n/a
6	CHD1	chr6:25043820-25044043	GM12878	blood:	n/a	n/a
7	EP300	chr6:25043146-25044281	GM12878	blood:	n/a	n/a
8	MEF2C	chr6:25043326-25044093	GM12878	blood:	n/a	n/a
9	MAZ	chr6:25043291-25043916	GM12878	blood:	n/a	n/a
10	TBL1XR1	chr6:25043348-25044003	GM12878	blood:	n/a	n/a
11	CUX1	chr6:25043303-25043928	GM12878	blood:	n/a	chr6:25043718-25043727
12	RUNX3	chr6:25042723-25044045	GM12878	blood:	n/a	n/a
13	EP300	chr6:25043172-25043987	GM12878	blood:	n/a	n/a
14	MTA3	chr6:25043159-25043925	GM12878	blood:	n/a	n/a
15	EBF1	chr6:25043251-25044243	GM12878	blood:	n/a	n/a
16	RELA	chr6:25043234-25043996	GM12878	blood:	n/a	n/a
17	TBP	chr6:25043178-25043967	GM12878	blood:	n/a	n/a
18	MEF2A	chr6:25043197-25043930	GM12878	blood:	n/a	n/a
19	MTA3	chr6:25042787-25043959	GM12878	blood:	n/a	n/a
20	WRNIP1	chr6:25043320-25044045	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FAM65B	TF binding region
ENSG00000272053	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11757374	0.84[CHD][hapmap]
rs12524842	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12525328	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525405	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12528227	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12661796	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12663160	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12665174	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13195161	0.92[ASN][1000 genomes]
rs13196712	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13203073	0.84[ASN][1000 genomes]
rs13218879	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1447243	0.81[ASN][1000 genomes]
rs1562422	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562423	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1597010	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1597011	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1597012	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs160034	0.84[ASN][1000 genomes]
rs1900551	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1923192	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1923193	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs192773	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs2273671	0.84[CHD][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap]
rs302992	0.84[ASN][1000 genomes]
rs303879	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs303880	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs303884	0.84[ASN][1000 genomes]
rs34475409	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34693126	0.88[ASN][1000 genomes]
rs35028017	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35553146	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36030790	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792974	1.00[YRI][hapmap]
rs3792983	0.87[CHD][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs3812108	0.84[CHD][hapmap]
rs4711071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711072	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56108659	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66577954	0.81[ASN][1000 genomes]
rs67240854	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67795839	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7738141	0.87[CHD][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs895676	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9348660	0.81[ASN][1000 genomes]
rs9358827	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9461093	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4712882	HIST1H3I	cis	parietal	SCAN
rs4712882	HIST1H1E	cis	parietal	SCAN
rs4712882	ZNF323	cis	parietal	SCAN
rs4712882	SLC17A4	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25035200-25044600	Weak transcription	Right Atrium	heart
2	chr6:25041800-25044000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:25042200-25050200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:25042400-25044200	Flanking Active TSS	GM12878-XiMat	blood
5	chr6:25042800-25044200	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:25042800-25044400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:25042800-25044400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:25043000-25044200	Enhancers	Primary T cells from cord blood	blood
9	chr6:25043000-25044200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:25043000-25044400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:25043000-25044400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:25043000-25044400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr6:25043000-25044600	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr6:25043000-25044600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:25043000-25044800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:25043000-25044800	Enhancers	Placenta	Placenta
17	chr6:25043200-25044000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr6:25043200-25044200	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:25043200-25044200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr6:25043200-25044400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr6:25043200-25044800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:25043200-25053400	Weak transcription	Spleen	Spleen
23	chr6:25043400-25044400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:25043400-25044600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:25043400-25050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:25043600-25044000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:25043800-25044400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:25043800-25050200	Weak transcription	Primary B cells from cord blood	blood

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