Variant report

Variant	rs2072653
Chromosome Location	chr17:18045098-18045099
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	RAD21	chr17:18044480-18045115	HCT-116	colon:	n/a	chr17:18044886-18044896
2	CTCF	chr17:18045020-18045170	GM12873	blood:	n/a	n/a
3	MAFK	chr17:18044985-18045178	K562	blood:	n/a	chr17:18045142-18045152
4	CTCF	chr17:18045040-18045190	GM12873	blood:	n/a	n/a
5	CTCF	chr17:18044980-18045130	HBMEC	blood vessel:	n/a	n/a
6	CTCF	chr17:18045080-18045230	A549	lung:	n/a	n/a
7	CTCF	chr17:18043985-18045480	A549	lung:	n/a	chr17:18045281-18045294
8	CTCF	chr17:18044980-18045130	K562	blood:	n/a	n/a
9	ELK1	chr17:18044527-18045179	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr17:18044960-18045110	AG04450	lung:	n/a	n/a
11	CTCF	chr17:18044166-18045329	SK-N-SH	brain:	n/a	chr17:18045281-18045294
12	CTCF	chr17:18044980-18045130	HepG2	liver:	n/a	n/a
13	RAD21	chr17:18044190-18045308	SK-N-SH	brain:	n/a	chr17:18044886-18044896 chr17:18045282-18045295
14	PAX5	chr17:18044862-18045116	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18045081..18047064-chr17:18085965..18088141,2	K562	blood:
2	chr17:18045055..18047545-chr17:18085965..18089684,5	K562	blood:
3	chr17:18044182..18045939-chr17:18050102..18052001,2	MCF-7	breast:
4	chr17:18044909..18046948-chr17:18057322..18059132,2	K562	blood:
5	chr17:18039043..18041825-chr17:18043264..18046470,4	K562	blood:
6	chr17:18044857..18048212-chr17:18048916..18052109,4	MCF-7	breast:
7	chr17:18039531..18041825-chr17:18044151..18046470,2	K562	blood:
8	chr17:18044679..18047861-chr17:18085770..18088322,3	MCF-7	breast:
9	chr17:18044317..18045124-chr17:18086070..18086665,2	MCF-7	breast:

Variant related genes	Relation type
MYO15A	TF binding region
ENSG00000238691	TF binding region
ENSG00000091542	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000091536	Chromatin interaction
ENSG00000238691	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1064629	0.83[EUR][1000 genomes]
rs12449609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12450483	0.84[AMR][1000 genomes]
rs2056841	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072652	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242595	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272571	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925145	0.82[CHD][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4925147	0.83[EUR][1000 genomes]
rs57186648	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58804619	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59179192	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72827432	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8068517	0.86[CEU][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription 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 miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv457697	chr17:18003845-18046290	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv574527	chr17:18003845-18046290	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv470580	chr17:18029857-18060192	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
13	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2072653	SNORD49B	cis	cerebellum	SCAN
rs2072653	SHMT1	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18039600-18046800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr17:18039800-18046200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:18040600-18056000	Weak transcription	Gastric	stomach
4	chr17:18040800-18056400	Weak transcription	Right Atrium	heart
5	chr17:18043400-18045200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr17:18043400-18046200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:18043600-18046800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr17:18044000-18046000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:18044200-18045400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
10	chr17:18044400-18045200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr17:18044400-18045200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr17:18044600-18045200	Enhancers	Brain Cingulate Gyrus	brain
13	chr17:18044600-18046400	Weak transcription	Pancreas	Pancrea
14	chr17:18044600-18046400	Weak transcription	HepG2	liver
15	chr17:18044600-18052200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:18044600-18053600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr17:18044800-18047200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr17:18045000-18045200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:18045000-18045200	Enhancers	Esophagus	oesophagus
20	chr17:18045000-18046200	Weak transcription	K562	blood
21	chr17:18045000-18046800	Weak transcription	Placenta	Placenta
22	chr17:18045000-18056600	Weak transcription	Fetal Intestine Small	intestine

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