Variant report

Variant	rs712273
Chromosome Location	chr17:18063441-18063442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr17:18062965-18063518	HepG2	liver:	n/a	n/a
2	MAZ	chr17:18063087-18063468	HepG2	liver:	n/a	n/a
3	EP300	chr17:18063256-18063699	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18059406..18063498-chr17:18086302..18089651,4	K562	blood:
2	chr17:18056639..18059705-chr17:18061625..18064659,3	MCF-7	breast:
3	chr17:18061742..18067292-chr17:18083221..18089651,7	K562	blood:
4	chr17:18061892..18063958-chr17:18064455..18066875,2	MCF-7	breast:

No data

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

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11869205	0.90[ASN][1000 genomes]
rs11870766	0.83[ASN][1000 genomes]
rs11871970	0.90[ASN][1000 genomes]
rs12150618	0.90[ASN][1000 genomes]
rs12451754	0.83[ASN][1000 genomes]
rs12936694	0.90[ASN][1000 genomes]
rs12939469	0.81[ASN][1000 genomes]
rs12946842	0.87[ASN][1000 genomes]
rs1378601	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1378602	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2360234	0.81[ASN][1000 genomes]
rs28641923	0.85[ASN][1000 genomes]
rs2925137	0.90[ASN][1000 genomes]
rs2925138	0.90[ASN][1000 genomes]
rs3794782	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924839	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924840	0.87[ASN][1000 genomes]
rs4924841	0.87[ASN][1000 genomes]
rs4925149	0.81[ASN][1000 genomes]
rs4925150	0.81[ASN][1000 genomes]
rs56021431	0.90[ASN][1000 genomes]
rs712275	0.85[ASN][1000 genomes]
rs7212808	0.86[ASN][1000 genomes]
rs8069321	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8071834	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854772	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854775	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854776	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs854779	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs854781	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs854795	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs854797	0.87[ASN][1000 genomes]
rs854798	0.92[ASN][1000 genomes]
rs854799	0.87[ASN][1000 genomes]
rs854801	0.90[ASN][1000 genomes]
rs854804	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854805	0.92[ASN][1000 genomes]
rs854806	0.92[ASN][1000 genomes]
rs854807	0.92[ASN][1000 genomes]
rs860568	0.87[ASN][1000 genomes]
rs865923	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
9	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
10	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
11	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs712273	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs712273	LGALS9C	cis	Whole Blood	GTEx
rs712273	TOP3A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18062000-18064400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr17:18062000-18064800	Weak transcription	Brain Anterior Caudate	brain
3	chr17:18062000-18065800	Enhancers	HSMM	muscle
4	chr17:18062000-18085600	Weak transcription	Brain Angular Gyrus	brain
5	chr17:18062200-18063600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr17:18062200-18063600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:18062200-18063600	Enhancers	NHDF-Ad	bronchial
8	chr17:18062200-18063600	Enhancers	NHLF	lung
9	chr17:18062200-18063600	Enhancers	Osteobl	bone
10	chr17:18062200-18063800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr17:18062200-18064600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr17:18062200-18065200	Enhancers	Fetal Muscle Leg	muscle
13	chr17:18062200-18065400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:18062200-18066600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr17:18062200-18067600	Enhancers	K562	blood
16	chr17:18062200-18085000	Weak transcription	Right Atrium	heart
17	chr17:18062400-18064200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:18062400-18064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:18062400-18064600	Weak transcription	Fetal Stomach	stomach
20	chr17:18062400-18066000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:18062400-18066000	Enhancers	GM12878-XiMat	blood
22	chr17:18062400-18066600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:18062600-18063600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:18062600-18063800	Enhancers	A549	lung
25	chr17:18062600-18064400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr17:18062600-18065400	Weak transcription	Spleen	Spleen
27	chr17:18062600-18070000	Weak transcription	Ovary	ovary
28	chr17:18062800-18063800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr17:18062800-18063800	Enhancers	NHEK	skin
30	chr17:18063000-18063600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr17:18063000-18064000	Enhancers	HepG2	liver
32	chr17:18063000-18064800	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr17:18063000-18065200	Enhancers	HSMMtube	muscle
34	chr17:18063200-18064400	Weak transcription	Liver	Liver
35	chr17:18063400-18063600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:18063400-18064400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr17:18063400-18064600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:18063400-18065400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:18063400-18066400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:18063400-18066400	Weak transcription	Fetal Intestine Large	intestine
41	chr17:18063400-18066400	Weak transcription	Fetal Intestine Small	intestine
42	chr17:18063400-18066600	Weak transcription	Placenta	Placenta

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