Variant report

Variant	rs12229266
Chromosome Location	chr12:42859739-42859740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42857420..42859847-chr12:42876771..42878949,2	K562	blood:
2	chr12:42858838..42861541-chr12:42866075..42868198,2	K562	blood:
3	chr12:42858889..42861856-chr12:42862365..42864970,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139174	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1043652	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1043656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880279	0.96[CEU][hapmap]
rs10880282	0.82[EUR][1000 genomes]
rs10880284	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs11181421	0.84[EUR][1000 genomes]
rs11181427	0.89[EUR][1000 genomes]
rs11181453	0.89[EUR][1000 genomes]
rs11181461	0.87[JPT][hapmap]
rs11181484	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11832772	0.81[CEU][hapmap]
rs12229224	0.87[EUR][1000 genomes]
rs12230583	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231335	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12422938	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12423383	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs12425945	0.96[CEU][hapmap]
rs12578312	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1376931	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1629725	0.91[EUR][1000 genomes]
rs1669884	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1669888	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1669890	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1669891	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1669894	0.91[EUR][1000 genomes]
rs1669895	0.91[EUR][1000 genomes]
rs1669897	0.91[EUR][1000 genomes]
rs1669898	0.91[EUR][1000 genomes]
rs1669899	0.89[EUR][1000 genomes]
rs1669900	0.91[EUR][1000 genomes]
rs1669901	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1669903	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1669905	0.91[EUR][1000 genomes]
rs1669911	0.89[EUR][1000 genomes]
rs1669912	0.91[EUR][1000 genomes]
rs1669913	0.91[EUR][1000 genomes]
rs1669914	0.91[EUR][1000 genomes]
rs1669935	0.91[EUR][1000 genomes]
rs1669937	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1796354	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1796355	0.91[EUR][1000 genomes]
rs1796356	0.91[EUR][1000 genomes]
rs1796357	0.96[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1796359	0.90[EUR][1000 genomes]
rs1796360	0.90[EUR][1000 genomes]
rs1796365	0.91[EUR][1000 genomes]
rs1796373	0.91[EUR][1000 genomes]
rs1796374	0.91[EUR][1000 genomes]
rs1796377	0.91[EUR][1000 genomes]
rs1796379	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1796385	0.91[EUR][1000 genomes]
rs1796387	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1796389	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1796392	0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1796395	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1796396	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1796397	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1796398	0.96[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053946	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2243465	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2406872	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406969	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2600911	0.91[EUR][1000 genomes]
rs2600912	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2600916	0.91[EUR][1000 genomes]
rs2600917	0.81[EUR][1000 genomes]
rs2600918	0.91[EUR][1000 genomes]
rs2708063	0.91[EUR][1000 genomes]
rs2708069	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2708075	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2708077	0.85[EUR][1000 genomes]
rs2708506	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2952653	0.91[EUR][1000 genomes]
rs3213989	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747563	0.96[EUR][1000 genomes]
rs3761677	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs3827524	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4603368	0.88[EUR][1000 genomes]
rs4768397	0.92[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs4768398	0.96[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs4768401	0.96[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs4768412	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7134895	1.00[CEU][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs721447	0.89[EUR][1000 genomes]
rs73122408	0.90[EUR][1000 genomes]
rs73122414	0.90[EUR][1000 genomes]
rs73122418	0.90[EUR][1000 genomes]
rs752767	0.91[EUR][1000 genomes]
rs896555	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs896556	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12229266	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42816800-42862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
3	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
4	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
5	chr12:42837200-42863200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:42840400-42860800	Weak transcription	Colonic Mucosa	Colon
7	chr12:42840600-42860000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:42841400-42862000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:42841600-42862400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:42843000-42862400	Weak transcription	Fetal Thymus	thymus
11	chr12:42843200-42862000	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:42843600-42862400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:42844800-42862600	Weak transcription	Primary T cells from cord blood	blood
14	chr12:42849400-42864800	Strong transcription	Fetal Stomach	stomach
15	chr12:42850000-42860800	Strong transcription	HSMMtube	muscle
16	chr12:42850000-42866400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:42850200-42859800	Strong transcription	Primary B cells from cord blood	blood
18	chr12:42850200-42860600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:42850200-42862800	Strong transcription	NH-A	brain
20	chr12:42850200-42865000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:42850200-42865000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:42850200-42865800	Strong transcription	Osteobl	bone
23	chr12:42850800-42860400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:42851400-42860800	Strong transcription	HSMM	muscle
25	chr12:42851800-42863000	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:42852000-42861400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:42852600-42862400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:42852800-42862800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:42853000-42862000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:42853400-42869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:42854000-42862400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:42854000-42863600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:42854000-42865800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr12:42854000-42868600	Weak transcription	Right Ventricle	heart
35	chr12:42854200-42865200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:42854200-42867400	Weak transcription	NHLF	lung
37	chr12:42854400-42864800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:42854400-42865200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:42854600-42864800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr12:42854800-42860600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:42855200-42864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:42855400-42864000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:42855400-42865200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:42855800-42860600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:42856000-42860000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:42856200-42860200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr12:42856200-42860600	Strong transcription	Fetal Lung	lung
48	chr12:42856200-42865800	Strong transcription	HMEC	breast
49	chr12:42856400-42859800	Strong transcription	Fetal Kidney	kidney
50	chr12:42856400-42860000	Genic enhancers	Fetal Heart	heart

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