Variant report

Variant	rs712274
Chromosome Location	chr17:18064195-18064196
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	MTA3	chr17:18063886-18064396	GM12878	blood:	n/a	n/a
2	BHLHE40	chr17:18064135-18064839	K562	blood:	n/a	n/a
3	MAX	chr17:18063705-18064970	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18056639..18059705-chr17:18061625..18064659,3	MCF-7	breast:
2	chr17:18061742..18067292-chr17:18083221..18089651,7	K562	blood:
3	chr17:18063606..18070028-chr17:18081885..18087934,10	MCF-7	breast:

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

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12051649	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12946752	0.86[GIH][hapmap]
rs1563632	0.86[GIH][hapmap]
rs1563634	0.86[GIH][hapmap]
rs2071241	0.84[MEX][hapmap];0.93[TSI][hapmap]
rs2075657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075658	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2245430	0.91[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs2473656	0.91[CHB][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2605133	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605141	0.86[GIH][hapmap]
rs2605144	0.87[GIH][hapmap]
rs2856289	0.86[EUR][1000 genomes]
rs4925144	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59588957	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712271	0.94[CEU][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7225932	0.86[GIH][hapmap]
rs72831919	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854773	0.94[CEU][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854774	0.94[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854777	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];0.86[TSI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854778	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs854780	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs854783	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs854796	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs854800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854803	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9899249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9903403	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9903591	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9913262	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs712274	SHMT1	cis	lymphoblastoid	seeQTL
rs712274	SHMT1	cis	Whole Blood	GTEx
rs712274	SHMT1	cis	Muscle Skeletal	GTEx
rs712274	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 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	chr17:18062200-18064600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:18062200-18065200	Enhancers	Fetal Muscle Leg	muscle
7	chr17:18062200-18065400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:18062200-18066600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr17:18062200-18067600	Enhancers	K562	blood
10	chr17:18062200-18085000	Weak transcription	Right Atrium	heart
11	chr17:18062400-18064200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr17:18062400-18064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:18062400-18064600	Weak transcription	Fetal Stomach	stomach
14	chr17:18062400-18066000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:18062400-18066000	Enhancers	GM12878-XiMat	blood
16	chr17:18062400-18066600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:18062600-18064400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:18062600-18065400	Weak transcription	Spleen	Spleen
19	chr17:18062600-18070000	Weak transcription	Ovary	ovary
20	chr17:18063000-18064800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr17:18063000-18065200	Enhancers	HSMMtube	muscle
22	chr17:18063200-18064400	Weak transcription	Liver	Liver
23	chr17:18063400-18064400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:18063400-18064600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:18063400-18065400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:18063400-18066400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr17:18063400-18066400	Weak transcription	Fetal Intestine Large	intestine
28	chr17:18063400-18066400	Weak transcription	Fetal Intestine Small	intestine
29	chr17:18063400-18066600	Weak transcription	Placenta	Placenta
30	chr17:18063600-18064600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:18063600-18064800	Weak transcription	Osteobl	bone
32	chr17:18063800-18064200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr17:18063800-18064600	Enhancers	Fetal Muscle Trunk	muscle

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