Variant report

Variant	rs888270
Chromosome Location	chr18:12774894-12774895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12772443..12775307-chr18:12781731..12784605,2	MCF-7	breast:
2	chr18:12774117..12776643-chr18:12883699..12885836,3	K562	blood:
3	chr18:12767228..12769677-chr18:12772403..12775378,2	K562	blood:
4	chr18:12760248..12761815-chr18:12774544..12776783,2	K562	blood:
5	chr18:12765202..12767798-chr18:12773652..12775696,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN2-1	chr18:12774650-12775922	ENSG00000260302.1
2	lnc-PTPN2-2	chr18:12774649-12775922	NONHSAT058393

No data

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction
ENSG00000201466	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11663253	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1893217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2014857	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2542147	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542148	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542149	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542150	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847259	1.00[ASN][1000 genomes]
rs2847260	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847274	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847278	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847280	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847293	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34920518	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs45450798	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60474474	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60735058	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60751993	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7237497	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8096138	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9952749	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1062149	chr18:12728115-12783898	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
9	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs888270	RP11-973H7.1	cis	Artery Tibial	GTEx
rs888270	RP11-973H7.1	cis	lung	GTEx
rs888270	RP11-973H7.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12767000-12776400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:12767400-12815800	Weak transcription	Gastric	stomach
3	chr18:12772000-12775000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr18:12772400-12775200	Weak transcription	HepG2	liver
5	chr18:12773000-12775000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr18:12773400-12776200	Active TSS	Thymus	Thymus
7	chr18:12773600-12775000	Active TSS	Fetal Thymus	thymus
8	chr18:12773800-12775000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr18:12774200-12776800	Active TSS	Dnd41	blood
10	chr18:12774600-12775200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr18:12774800-12775000	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr18:12774800-12775000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr18:12774800-12775200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr18:12774800-12776200	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr18:12774800-12776200	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr18:12774800-12776200	Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr18:12774800-12776200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr18:12774800-12777600	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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