Variant report

Variant	rs854775
Chromosome Location	chr17:18050888-18050889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18049467..18051833-chr17:18057367..18059688,2	MCF-7	breast:
2	chr17:18044182..18045939-chr17:18050102..18052001,2	MCF-7	breast:
3	chr17:18050664..18054288-chr17:18086112..18089564,5	K562	blood:
4	chr17:18050664..18053443-chr17:18085067..18087768,3	K562	blood:

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

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11870766	0.88[JPT][hapmap]
rs12150618	0.88[JPT][hapmap]
rs12936694	0.86[JPT][hapmap]
rs12939469	0.86[JPT][hapmap]
rs1378601	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs1378602	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2360234	0.86[JPT][hapmap]
rs3794782	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4603612	0.86[JPT][hapmap]
rs4924839	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs4924840	0.88[JPT][hapmap]
rs4924841	0.86[JPT][hapmap]
rs712270	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs712272	0.88[ASN][1000 genomes]
rs712273	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8069321	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8071834	0.88[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs854771	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs854772	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854776	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854779	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs854781	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs854795	0.96[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854798	0.80[ASN][1000 genomes]
rs854804	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854805	0.80[ASN][1000 genomes]
rs854806	0.80[ASN][1000 genomes]
rs854807	0.80[ASN][1000 genomes]
rs860567	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs860568	0.86[JPT][hapmap]
rs861278	0.83[ASN][1000 genomes]
rs865923	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs854775	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 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	chr17:18048400-18051400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:18048600-18056000	Weak transcription	Pancreas	Pancrea
13	chr17:18049000-18055600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr17:18049600-18052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:18050400-18052000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:18050800-18056000	Weak transcription	Placenta	Placenta

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