Variant report

Variant	rs854800
Chromosome Location	chr17:18077175-18077176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18076110..18077734-chr17:18086382..18087948,2	MCF-7	breast:
2	chr17:18072868..18077366-chr17:18083482..18088820,6	K562	blood:
3	chr17:18075390..18078535-chr17:18084220..18086756,4	MCF-7	breast:
4	chr17:18060022..18062272-chr17:18076664..18079506,2	K562	blood:
5	chr17:18075465..18077219-chr17:18087320..18089621,2	K562	blood:

Variant related genes	Relation type
ENSG00000091536	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000266677	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12051649	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12946752	0.84[GIH][hapmap]
rs1563632	0.84[GIH][hapmap]
rs1563634	0.84[GIH][hapmap]
rs2071241	0.83[TSI][hapmap]
rs2075657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075658	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2245430	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs2280777	0.81[CHD][hapmap]
rs2473656	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs2605133	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605141	0.84[GIH][hapmap]
rs2605144	0.85[GIH][hapmap]
rs2856289	0.80[EUR][1000 genomes]
rs4925144	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59588957	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712271	0.94[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs712274	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]
rs7225932	0.84[GIH][hapmap]
rs72831919	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854773	0.94[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854774	0.94[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854777	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854778	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs854780	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs854783	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs854796	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[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];0.99[ASN][1000 genomes]
rs854803	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9899249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9903403	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9903591	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9913262	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs854800	SHMT1	cis	Esophagus Muscularis	GTEx
rs854800	LOC162632	cis	parietal	SCAN
rs854800	LOC162632	cis	cerebellum	SCAN
rs854800	SHMT1	cis	parietal	SCAN
rs854800	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs854800	SHMT1	cis	lymphoblastoid	seeQTL
rs854800	TOP3A	cis	cerebellum	SCAN
rs854800	SHMT1	cis	Whole Blood	GTEx
rs854800	MYO15A	cis	parietal	SCAN
rs854800	MYO15A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18062000-18085600	Weak transcription	Brain Angular Gyrus	brain
2	chr17:18062200-18085000	Weak transcription	Right Atrium	heart
3	chr17:18064800-18085400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:18071200-18084800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:18071800-18082000	Weak transcription	Fetal Intestine Small	intestine
6	chr17:18072400-18085400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:18072800-18085000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr17:18075600-18079000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:18075600-18085400	Weak transcription	Brain Germinal Matrix	brain
10	chr17:18075800-18084400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:18075800-18085200	Weak transcription	Right Ventricle	heart
12	chr17:18076000-18085400	Weak transcription	Esophagus	oesophagus
13	chr17:18076000-18086000	Weak transcription	Ovary	ovary
14	chr17:18076200-18077800	Enhancers	Duodenum Mucosa	Duodenum
15	chr17:18076200-18078200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr17:18076200-18084600	Weak transcription	Fetal Stomach	stomach
17	chr17:18076600-18082400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr17:18076600-18085000	Weak transcription	Pancreas	Pancrea
19	chr17:18076800-18077400	Enhancers	Spleen	Spleen
20	chr17:18076800-18078200	Enhancers	Liver	Liver
21	chr17:18076800-18083200	Weak transcription	K562	blood
22	chr17:18076800-18084400	Weak transcription	Fetal Muscle Leg	muscle

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