Variant report

Variant	rs4458754
Chromosome Location	chr7:12613059-12613060
allele	C/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	SPI1	chr7:12612575-12613182	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:12603978..12606126-chr7:12612783..12614371,2	K562	blood:
2	chr7:12609604..12611668-chr7:12611750..12616186,4	MCF-7	breast:
3	chr7:12612509..12614606-chr7:12725863..12728271,2	K562	blood:

Variant related genes	Relation type
ENSG00000225606	TF binding region
ENSG00000225606	Chromatin interaction
ENSG00000006747	Chromatin interaction
ENSG00000122644	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1034856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1118998	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11558844	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11973033	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17283696	0.89[CEU][hapmap]
rs17283717	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17355921	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1990224	0.85[CEU][hapmap]
rs1990225	0.85[CEU][hapmap]
rs2240572	0.89[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2240574	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3735222	0.92[CEU][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3735223	0.92[CEU][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41356146	0.92[CEU][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41379149	0.84[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs55682719	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55829483	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55999874	0.84[ASN][1000 genomes]
rs56085455	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56131067	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56274604	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56760264	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57778115	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460964	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6460965	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs6954111	0.82[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs6961909	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6965970	0.92[CEU][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6967031	0.83[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6972418	0.84[ASN][1000 genomes]
rs73060662	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73060664	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73060678	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73060679	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73060680	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73060684	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73060686	0.82[ASN][1000 genomes]
rs73062610	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73062611	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73062639	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782451	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7799976	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7803810	0.92[CEU][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7804260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7811582	0.88[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv528031	chr7:12536336-12618764	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1025006	chr7:12543161-12618924	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1027831	chr7:12543161-12619740	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv470066	chr7:12543794-12618764	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1033478	chr7:12547121-12618924	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv464379	chr7:12572742-12618764	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv606231	chr7:12572742-12618764	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4458754	ZC3H15	trans	parietal	SCAN
rs4458754	SOSTDC1	cis	cerebellum	SCAN
rs4458754	SCIN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12610400-12613400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr7:12611000-12613200	Active TSS	Duodenum Mucosa	Duodenum
3	chr7:12611200-12613200	Enhancers	Adipose Nuclei	Adipose
4	chr7:12611600-12613600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:12611600-12620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:12611800-12637600	Weak transcription	Colonic Mucosa	Colon
7	chr7:12612000-12613800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:12612000-12622000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:12612600-12613400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:12612600-12613400	Active TSS	Fetal Kidney	kidney
11	chr7:12612800-12613200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:12612800-12613200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr7:12612800-12613400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr7:12613000-12613200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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