Variant report

Variant	rs73122408
Chromosome Location	chr12:42753937-42753938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42752516..42754157-chr12:42754165..42756089,3	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1043652	0.91[EUR][1000 genomes]
rs1043656	0.90[EUR][1000 genomes]
rs10880282	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880284	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181421	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181427	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11181453	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181461	0.99[ASN][1000 genomes]
rs11181484	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12229224	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12229266	0.90[EUR][1000 genomes]
rs12230583	0.90[EUR][1000 genomes]
rs12231335	0.88[EUR][1000 genomes]
rs12422938	0.90[EUR][1000 genomes]
rs12423383	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425945	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12578312	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1376931	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1629725	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669884	0.92[EUR][1000 genomes]
rs1669888	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669890	0.97[EUR][1000 genomes]
rs1669891	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669894	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669895	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669897	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669898	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669899	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669900	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669901	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669903	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669905	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669912	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669913	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669914	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669935	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669937	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17091052	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796354	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796355	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796356	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796357	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1796359	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796360	0.99[EUR][1000 genomes]
rs1796365	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796373	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796374	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796377	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796379	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796385	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796387	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796389	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796392	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1796395	0.96[EUR][1000 genomes]
rs1796396	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796397	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1796398	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1961953	0.84[EUR][1000 genomes]
rs2053946	0.89[EUR][1000 genomes]
rs2061191	0.81[EUR][1000 genomes]
rs2061192	0.80[EUR][1000 genomes]
rs2243465	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2406872	0.88[EUR][1000 genomes]
rs2406969	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2600911	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2600912	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2600916	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2600917	0.90[EUR][1000 genomes]
rs2600918	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2708063	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2708069	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708075	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708077	0.92[EUR][1000 genomes]
rs2708506	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952653	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3213989	0.88[EUR][1000 genomes]
rs3747563	0.91[EUR][1000 genomes]
rs3761677	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827524	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603368	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768397	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768398	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768401	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768412	0.89[EUR][1000 genomes]
rs7134895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721447	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7298965	0.81[EUR][1000 genomes]
rs73122414	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73122418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486516	0.84[EUR][1000 genomes]
rs752767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896555	0.96[EUR][1000 genomes]
rs896556	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs73122408	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721000-42758000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:42721600-42769000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:42721600-42778600	Weak transcription	Spleen	Spleen
5	chr12:42721600-42800800	Weak transcription	Psoas Muscle	Psoas
6	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:42721800-42756200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:42721800-42769600	Weak transcription	Brain Substantia Nigra	brain
9	chr12:42721800-42769800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:42721800-42797000	Weak transcription	NHLF	lung
11	chr12:42721800-42803600	Weak transcription	Gastric	stomach
12	chr12:42722000-42769600	Weak transcription	Brain Anterior Caudate	brain
13	chr12:42722000-42769600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:42722000-42772600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:42722000-42793200	Weak transcription	Fetal Kidney	kidney
16	chr12:42722200-42769200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:42724400-42755400	Weak transcription	Pancreas	Pancrea
18	chr12:42730800-42769600	Weak transcription	NH-A	brain
19	chr12:42731000-42757400	Weak transcription	Brain Germinal Matrix	brain
20	chr12:42731000-42768800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:42731200-42754000	Weak transcription	HUVEC	blood vessel
22	chr12:42731400-42769600	Weak transcription	Fetal Lung	lung
23	chr12:42731800-42770400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:42732000-42754200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:42732000-42754200	Weak transcription	Lung	lung
26	chr12:42732200-42781200	Weak transcription	Fetal Brain Female	brain
27	chr12:42732200-42794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:42732400-42763600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr12:42732400-42769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:42733400-42796800	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:42738000-42754000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:42738000-42787400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:42742000-42758400	Weak transcription	Stomach Mucosa	stomach
35	chr12:42742600-42758800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:42743000-42755000	Weak transcription	Brain Angular Gyrus	brain
37	chr12:42743200-42755600	Weak transcription	NHEK	skin
38	chr12:42745200-42758800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:42746000-42757000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:42746000-42778400	Weak transcription	Fetal Brain Male	brain
41	chr12:42746600-42769800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:42747400-42768800	Weak transcription	NHDF-Ad	bronchial
43	chr12:42747600-42769000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:42748200-42763600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:42748400-42757400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:42750200-42756600	Weak transcription	Fetal Intestine Small	intestine
47	chr12:42750200-42762000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:42750400-42754000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:42750400-42754400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:42750400-42754600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links