Variant report

Variant	rs854774
Chromosome Location	chr17:18051975-18051976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18044182..18045939-chr17:18050102..18052001,2	MCF-7	breast:
2	chr17:18050664..18054288-chr17:18086112..18089564,5	K562	blood:
3	chr17:18050664..18053443-chr17:18085067..18087768,3	K562	blood:

Variant related genes	Relation type
ENSG00000091542	Chromatin interaction
ENSG00000266677	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12051649	0.82[EUR][1000 genomes]
rs2071241	0.85[TSI][hapmap]
rs2075657	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2075658	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245430	0.83[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2280777	0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2473656	0.83[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs2605133	0.81[EUR][1000 genomes]
rs2856289	0.81[EUR][1000 genomes]
rs4925144	0.89[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59588957	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs712271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712274	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]
rs72831919	0.83[EUR][1000 genomes]
rs854773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854777	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs854778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs854780	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs854782	0.91[ASN][1000 genomes]
rs854783	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854784	0.92[ASN][1000 genomes]
rs854796	0.81[ASN][1000 genomes]
rs854800	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]
rs854802	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];0.80[ASN][1000 genomes]
rs854803	1.00[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9899249	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs9903403	0.84[EUR][1000 genomes]
rs9903591	0.84[EUR][1000 genomes]
rs9913262	0.88[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
11	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
12	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs854774	SHMT1	cis	parietal	SCAN
rs854774	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs854774	MYO15A	cis	cerebellum	SCAN
rs854774	MYO15A	cis	parietal	SCAN
rs854774	SHMT1	cis	Esophagus Muscularis	GTEx
rs854774	LOC162632	cis	cerebellum	SCAN
rs854774	SHMT1	cis	lymphoblastoid	seeQTL
rs854774	FLJ36492	cis	multi-tissue	Pritchard
rs854774	LOC162632	cis	parietal	SCAN
rs854774	SHMT1	cis	multi-tissue	Pritchard
rs854774	TOP3A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18040600-18056000	Weak transcription	Gastric	stomach
2	chr17:18040800-18056400	Weak transcription	Right Atrium	heart
3	chr17:18044600-18052200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:18044600-18053600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr17:18045000-18056600	Weak transcription	Fetal Intestine Small	intestine
6	chr17:18045200-18056600	Weak transcription	Esophagus	oesophagus
7	chr17:18046600-18056000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr17:18047200-18054400	Weak transcription	Lung	lung
9	chr17:18047400-18054000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:18047400-18056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:18048600-18056000	Weak transcription	Pancreas	Pancrea
12	chr17:18049000-18055600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr17:18049600-18052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:18050400-18052000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:18050800-18056000	Weak transcription	Placenta	Placenta
16	chr17:18051400-18054200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:18051600-18056000	Weak transcription	Ovary	ovary
18	chr17:18051800-18052200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr17:18051800-18056000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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