Variant report

Variant	rs1669898
Chromosome Location	chr12:42803375-42803376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42802234..42803947-chr12:42811454..42813623,2	K562	blood:
2	chr12:42801580..42805588-chr12:42807427..42809707,3	K562	blood:
3	chr12:42802678..42804197-chr12:42822654..42825648,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1043652	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043656	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs10880275	0.92[CEU][hapmap]
rs10880279	0.92[CEU][hapmap]
rs10880282	0.88[EUR][1000 genomes]
rs10880284	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11181421	0.92[EUR][1000 genomes]
rs11181427	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11181453	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11181484	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12229224	0.96[EUR][1000 genomes]
rs12229266	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12230583	0.91[EUR][1000 genomes]
rs12231335	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs12422938	0.90[EUR][1000 genomes]
rs12423383	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12425945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12578312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1376931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1629725	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669888	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1669890	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669891	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669895	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669897	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669899	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669901	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669903	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669905	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669911	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669914	1.00[EUR][1000 genomes]
rs1669935	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091052	0.83[EUR][1000 genomes]
rs1796354	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1796355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1796356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796357	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796359	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796360	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1796365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796373	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796374	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796377	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796379	0.99[EUR][1000 genomes]
rs1796385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796387	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796389	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796392	0.93[EUR][1000 genomes]
rs1796395	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796396	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1796397	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1796398	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1961953	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2053946	0.89[EUR][1000 genomes]
rs2061191	0.81[EUR][1000 genomes]
rs2243465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2406872	0.89[EUR][1000 genomes]
rs2406969	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2600911	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2600912	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2600916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2600917	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2600918	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708069	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2708075	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2708077	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708506	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2952653	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213989	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3747562	0.81[CEU][hapmap]
rs3747563	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3761677	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3827524	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4603368	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768397	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4768398	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4768401	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs4768412	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs6582392	0.92[CEU][hapmap]
rs7134895	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs721447	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298965	0.81[EUR][1000 genomes]
rs73122408	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73122414	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73122418	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7486516	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs752767	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7956016	0.80[CEU][hapmap]
rs7960176	0.92[CEU][hapmap]
rs7975518	0.80[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs896555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs896556	0.82[AMR][1000 genomes];0.97[EUR][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
rs1669898	PPHLN1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:42721800-42803600	Weak transcription	Gastric	stomach
4	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:42763800-42804200	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:42767200-42836200	Weak transcription	Esophagus	oesophagus
7	chr12:42770200-42815800	Weak transcription	Fetal Lung	lung
8	chr12:42770400-42816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:42780200-42836000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:42780400-42804200	Weak transcription	K562	blood
11	chr12:42780400-42811200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:42782800-42803400	Weak transcription	Spleen	Spleen
13	chr12:42782800-42804200	Weak transcription	Fetal Brain Female	brain
14	chr12:42782800-42807200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:42783000-42836000	Weak transcription	Lung	lung
16	chr12:42785400-42836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:42789600-42812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:42789600-42836200	Weak transcription	Pancreas	Pancrea
19	chr12:42790600-42803800	Weak transcription	Colonic Mucosa	Colon
20	chr12:42793200-42806800	Weak transcription	Brain Substantia Nigra	brain
21	chr12:42793800-42803400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:42793800-42840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:42794400-42803800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:42794800-42804200	Weak transcription	Fetal Kidney	kidney
25	chr12:42795000-42813600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:42795400-42804000	Weak transcription	Placenta	Placenta
27	chr12:42795400-42834600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:42795600-42806000	Weak transcription	Primary T cells from cord blood	blood
29	chr12:42795600-42811400	Weak transcription	Adipose Nuclei	Adipose
30	chr12:42795600-42811800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:42795600-42820400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:42795600-42820600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:42795600-42825800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:42795600-42834400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:42795800-42821800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:42795800-42836000	Weak transcription	Thymus	Thymus
37	chr12:42796000-42803800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:42796000-42804200	Weak transcription	Fetal Intestine Small	intestine
39	chr12:42796000-42805000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:42796000-42806400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:42796000-42807600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:42796000-42812800	Weak transcription	Osteobl	bone
43	chr12:42796000-42813400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:42796000-42819600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:42796000-42820400	Weak transcription	NHEK	skin
46	chr12:42796000-42823600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:42796000-42825600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:42796000-42825800	Weak transcription	Left Ventricle	heart
49	chr12:42796000-42833200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:42796000-42834400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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