Variant report

Variant	rs10880284
Chromosome Location	chr12:42710424-42710425
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42709563..42711250-chr12:42718047..42720183,2	K562	blood:
2	chr12:42707619..42711063-chr12:42718047..42720920,3	K562	blood:
3	chr12:42710045..42713783-chr12:42716429..42721325,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134283	Chromatin interaction
ENSG00000139168	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1043652	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1043656	0.96[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs1069644	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10785337	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880275	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs10880279	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs10880280	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880282	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181421	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181427	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11181453	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11181484	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1118483	0.81[EUR][1000 genomes]
rs12229224	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12229266	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs12230583	0.82[EUR][1000 genomes]
rs12231335	0.91[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs1238290	0.80[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs12422938	0.81[EUR][1000 genomes]
rs12423383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425945	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12578312	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1376931	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1629725	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669884	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1669888	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1669890	0.87[EUR][1000 genomes]
rs1669891	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669894	0.89[EUR][1000 genomes]
rs1669895	0.89[EUR][1000 genomes]
rs1669897	0.89[EUR][1000 genomes]
rs1669898	0.89[EUR][1000 genomes]
rs1669899	0.88[EUR][1000 genomes]
rs1669900	0.89[EUR][1000 genomes]
rs1669901	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669905	0.89[EUR][1000 genomes]
rs1669911	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669912	0.89[EUR][1000 genomes]
rs1669913	0.89[EUR][1000 genomes]
rs1669914	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669935	0.89[EUR][1000 genomes]
rs1669937	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1683195	0.80[CEU][hapmap]
rs17091052	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1796354	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1796355	0.89[EUR][1000 genomes]
rs1796356	0.89[EUR][1000 genomes]
rs1796357	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1796359	0.89[EUR][1000 genomes]
rs1796360	0.89[EUR][1000 genomes]
rs1796365	0.89[EUR][1000 genomes]
rs1796373	0.89[EUR][1000 genomes]
rs1796374	0.89[EUR][1000 genomes]
rs1796377	0.89[EUR][1000 genomes]
rs1796379	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796385	0.89[EUR][1000 genomes]
rs1796387	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1796395	0.86[EUR][1000 genomes]
rs1796396	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796397	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1796398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1961953	0.89[EUR][1000 genomes]
rs2053946	0.81[EUR][1000 genomes]
rs2061191	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2061192	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2198763	0.82[EUR][1000 genomes]
rs2243465	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2406872	0.80[EUR][1000 genomes]
rs2406969	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2600911	0.89[EUR][1000 genomes]
rs2600912	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2600916	0.89[EUR][1000 genomes]
rs2600917	0.82[EUR][1000 genomes]
rs2600918	0.89[EUR][1000 genomes]
rs2708063	0.89[EUR][1000 genomes]
rs2708069	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708075	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708077	0.82[EUR][1000 genomes]
rs2708506	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2952653	0.89[EUR][1000 genomes]
rs3213989	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs3747562	0.81[CEU][hapmap]
rs3747563	0.81[EUR][1000 genomes]
rs3761677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4603368	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768397	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768398	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768412	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs6582389	0.81[ASN][1000 genomes]
rs6582392	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs712119	0.80[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs712120	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs712122	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs712123	0.80[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs712125	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs712129	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs7134895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs721447	0.88[EUR][1000 genomes]
rs7298965	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73122408	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73122414	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73122418	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7486516	0.89[EUR][1000 genomes]
rs752767	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7956016	0.80[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs7959339	0.82[EUR][1000 genomes]
rs7960176	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs7970115	0.92[CHB][hapmap]
rs7975518	0.80[CEU][hapmap]
rs824738	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs824741	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs896555	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs896556	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10880284	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42693600-42719000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:42695200-42710600	Weak transcription	GM12878-XiMat	blood
3	chr12:42695600-42714800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:42696200-42718800	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:42697000-42718800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:42697200-42710600	Weak transcription	Ovary	ovary
7	chr12:42697400-42718000	Weak transcription	HepG2	liver
8	chr12:42699600-42718800	Weak transcription	HUVEC	blood vessel
9	chr12:42699800-42718200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:42700800-42716400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:42701200-42718600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:42701400-42717400	Weak transcription	Pancreas	Pancrea
13	chr12:42701800-42712200	Weak transcription	Thymus	Thymus
14	chr12:42701800-42718600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:42701800-42718800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:42701800-42719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:42702200-42718600	Weak transcription	Brain Substantia Nigra	brain
18	chr12:42702400-42714600	Weak transcription	Brain Germinal Matrix	brain
19	chr12:42702600-42718800	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:42702800-42712200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:42703000-42717400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:42703800-42715000	Weak transcription	Hela-S3	cervix
23	chr12:42703800-42718800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:42704200-42718400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:42704800-42712400	Weak transcription	Lung	lung
26	chr12:42705000-42711600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:42705000-42712000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:42705000-42718000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:42705200-42711600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:42705200-42714800	Weak transcription	Fetal Lung	lung
31	chr12:42705200-42718600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:42705200-42718600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:42705200-42719000	Weak transcription	HSMMtube	muscle
34	chr12:42705400-42718400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:42705400-42719200	Weak transcription	Fetal Intestine Small	intestine
36	chr12:42705600-42711800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:42705600-42713000	Strong transcription	Liver	Liver
38	chr12:42705600-42714600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:42705600-42719200	Weak transcription	Psoas Muscle	Psoas
40	chr12:42705600-42719400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:42705600-42719400	Weak transcription	Small Intestine	intestine
42	chr12:42705800-42712600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:42705800-42716400	Weak transcription	NHDF-Ad	bronchial
44	chr12:42705800-42718400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:42705800-42718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:42705800-42719400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:42706000-42711600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:42706000-42711800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:42706000-42711800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:42706000-42712000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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