Variant report

Variant	rs1961953
Chromosome Location	chr12:42692916-42692917
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42656814..42658836-chr12:42692497..42694182,2	K562	blood:
2	chr12:42691640..42695316-chr12:42718541..42721156,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134283	Chromatin interaction
ENSG00000139168	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1043652	0.87[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10785335	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10785337	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10880275	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880279	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10880280	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10880282	0.90[EUR][1000 genomes]
rs10880284	0.89[EUR][1000 genomes]
rs11181421	0.87[EUR][1000 genomes]
rs11181427	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11181453	0.83[EUR][1000 genomes]
rs11181484	0.82[EUR][1000 genomes]
rs1118483	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12229224	0.80[EUR][1000 genomes]
rs12423383	0.89[EUR][1000 genomes]
rs12425945	0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12578312	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1376931	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1629725	0.83[EUR][1000 genomes]
rs1669884	0.88[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1669890	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1669891	0.81[EUR][1000 genomes]
rs1669894	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1669895	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1669897	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1669898	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1669899	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1669900	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1669901	0.83[EUR][1000 genomes]
rs1669903	0.83[EUR][1000 genomes]
rs1669905	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1669911	0.82[EUR][1000 genomes]
rs1669912	0.83[EUR][1000 genomes]
rs1669913	0.83[EUR][1000 genomes]
rs1669914	0.83[EUR][1000 genomes]
rs1669935	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1669937	0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1683195	0.87[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs17091052	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796355	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1796356	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1796357	0.83[EUR][1000 genomes]
rs1796359	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1796360	0.83[EUR][1000 genomes]
rs1796365	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1796373	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1796374	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1796377	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1796379	0.84[EUR][1000 genomes]
rs1796385	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1796387	0.82[EUR][1000 genomes]
rs1796389	0.83[EUR][1000 genomes]
rs1796395	0.81[ASN][1000 genomes]
rs1796397	0.80[EUR][1000 genomes]
rs1796398	0.81[EUR][1000 genomes]
rs2061191	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2061192	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2085314	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2198763	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2243465	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2600911	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2600912	0.83[EUR][1000 genomes]
rs2600916	0.83[EUR][1000 genomes]
rs2600918	0.83[EUR][1000 genomes]
rs2605401	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2708063	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2708069	0.83[EUR][1000 genomes]
rs2708075	0.83[EUR][1000 genomes]
rs2708506	0.83[EUR][1000 genomes]
rs2952653	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3747563	0.80[ASN][1000 genomes]
rs3761677	0.89[EUR][1000 genomes]
rs3827524	0.85[EUR][1000 genomes]
rs4402364	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4417370	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4603368	0.82[EUR][1000 genomes]
rs4768397	0.89[EUR][1000 genomes]
rs4768398	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768401	0.83[EUR][1000 genomes]
rs6582386	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6582392	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs712126	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs712127	0.85[AMR][1000 genomes]
rs7134895	0.83[EUR][1000 genomes]
rs721447	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7298965	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73122408	0.84[EUR][1000 genomes]
rs73122414	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73122418	0.84[EUR][1000 genomes]
rs7486516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752767	0.83[EUR][1000 genomes]
rs7959339	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7960176	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7975518	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs824742	0.84[AMR][1000 genomes]
rs896555	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
5	esv1809322	chr12:42682065-42699107	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1961953	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42690800-42706400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:42692400-42693000	Flanking Active TSS	GM12878-XiMat	blood
3	chr12:42692400-42693600	Enhancers	HepG2	liver
4	chr12:42692800-42693400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:42692800-42693800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr12:42692800-42694000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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