Variant report

Variant	rs17535998
Chromosome Location	chr10:92753721-92753722
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	MTA3	chr10:92753075-92753875	GM12878	blood:	n/a	n/a
2	PML	chr10:92752995-92754193	GM12878	blood:	n/a	n/a
3	MEF2A	chr10:92752094-92753756	GM12878	blood:	n/a	n/a
4	MTA3	chr10:92753069-92753846	GM12878	blood:	n/a	n/a
5	RUNX3	chr10:92752810-92754416	GM12878	blood:	n/a	n/a
6	STAT5A	chr10:92753052-92753771	GM12878	blood:	n/a	n/a
7	RCOR1	chr10:92753255-92753736	GM12878	blood:	n/a	n/a
8	MXI1	chr10:92753716-92754499	GM12878	blood:	n/a	n/a
9	BCLAF1	chr10:92753441-92753795	GM12878	blood:	n/a	n/a
10	MEF2C	chr10:92752931-92753722	GM12878	blood:	n/a	chr10:92753358-92753373 chr10:92753319-92753334
11	NFIC	chr10:92752791-92753780	GM12878	blood:	n/a	n/a
12	NFIC	chr10:92751803-92754094	GM12878	blood:	n/a	n/a
13	RELA	chr10:92752941-92753732	GM12878	blood:	n/a	n/a
14	EP300	chr10:92752853-92753879	GM12878	blood:	n/a	n/a
15	IKZF1	chr10:92753193-92753865	GM12878	blood:	n/a	n/a
16	RUNX3	chr10:92753027-92753857	GM12878	blood:	n/a	n/a
17	FOXM1	chr10:92752793-92753781	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:92748134..92750120-chr10:92751993..92753811,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225519	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs17103779	0.88[ASN][1000 genomes]
rs17456916	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17536094	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17536636	1.00[AFR][1000 genomes]
rs55863711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55886424	1.00[ASN][1000 genomes]
rs56075405	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56226914	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56242242	1.00[ASN][1000 genomes]
rs56285679	1.00[ASN][1000 genomes]
rs56342917	1.00[ASN][1000 genomes]
rs56374954	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56954792	1.00[ASN][1000 genomes]
rs61857869	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61857871	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs61859572	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61859573	0.81[AMR][1000 genomes]
rs61859574	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61859575	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61859576	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61859580	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61859604	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61859605	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61859606	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61859607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61859608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61859609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61859610	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61859611	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61859612	1.00[ASN][1000 genomes]
rs61859613	1.00[ASN][1000 genomes]
rs61859614	1.00[ASN][1000 genomes]
rs61859616	1.00[ASN][1000 genomes]
rs61859617	1.00[ASN][1000 genomes]
rs61859618	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7074584	0.82[EUR][1000 genomes]
rs7083785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7083909	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906136	0.91[ASN][1000 genomes]
rs7912022	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914213	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831945	chr10:92590576-92793582	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17535998	IDE	cis	parietal	SCAN
rs17535998	DKC1	trans	cerebellum	SCAN
rs17535998	FGFBP3	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92744200-92766200	Weak transcription	Right Ventricle	heart
2	chr10:92748000-92755200	Enhancers	Dnd41	blood
3	chr10:92748000-92758600	Weak transcription	Right Atrium	heart
4	chr10:92749800-92753800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr10:92749800-92753800	Weak transcription	Thymus	Thymus
6	chr10:92751600-92760200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:92752000-92754400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:92752000-92754800	Enhancers	NHDF-Ad	bronchial
9	chr10:92752800-92754400	Enhancers	HSMMtube	muscle
10	chr10:92752800-92754600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr10:92752800-92754600	Enhancers	HSMM	muscle
12	chr10:92753000-92753800	Active TSS	GM12878-XiMat	blood
13	chr10:92753000-92754600	Enhancers	Osteobl	bone
14	chr10:92753400-92753800	Enhancers	Primary B cells from peripheral blood	blood
15	chr10:92753600-92754000	Enhancers	Left Ventricle	heart
16	chr10:92753600-92754000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr10:92753600-92754200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr10:92753600-92754200	Enhancers	Fetal Thymus	thymus
19	chr10:92753600-92754600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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