Variant report

Variant	rs61918809
Chromosome Location	chr12:48488355-48488356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10219623	0.80[AMR][1000 genomes]
rs10875730	0.81[AFR][1000 genomes]
rs10875731	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10875732	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10875735	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875736	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875737	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875738	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875740	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875745	0.80[AMR][1000 genomes]
rs10875746	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10875747	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10875748	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10875750	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10875756	0.83[EUR][1000 genomes]
rs11168369	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11168370	0.80[EUR][1000 genomes]
rs11168374	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11168383	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168386	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168401	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168403	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168413	0.80[AMR][1000 genomes]
rs11168414	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11168418	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168420	0.92[EUR][1000 genomes]
rs11168422	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11168427	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168433	0.83[EUR][1000 genomes]
rs12296244	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12297004	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12297470	0.80[AMR][1000 genomes]
rs12301339	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12304476	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306451	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12310813	0.80[AMR][1000 genomes]
rs12310999	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12311774	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12311953	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12313300	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12313404	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12315625	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17122620	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17122666	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1859445	0.80[AMR][1000 genomes]
rs2107638	0.80[AMR][1000 genomes]
rs2158516	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228500	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2269935	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2269936	0.81[AFR][1000 genomes]
rs2286021	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3782910	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782911	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760680	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4760681	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4760689	0.83[EUR][1000 genomes]
rs4760690	0.83[EUR][1000 genomes]
rs58952582	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60761335	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61918774	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61918806	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61918810	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs725454	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73102065	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73102067	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7485355	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8804	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs886588	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs989144	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs61918809	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs61918809	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs61918809	RP1-228P16.1	cis	Artery Tibial	GTEx
rs61918809	RP1-228P16.1	cis	Thyroid	GTEx
rs61918809	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
9	chr12:48470800-48492800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:48471400-48492000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:48472200-48489400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:48472400-48492000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:48472600-48490200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:48472600-48490200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:48472600-48493600	Strong transcription	Fetal Thymus	thymus
16	chr12:48472800-48493800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:48473000-48494800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:48473200-48492000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:48473600-48490000	Strong transcription	Primary T cells from cord blood	blood
20	chr12:48473600-48495400	Strong transcription	Dnd41	blood
21	chr12:48473800-48491600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr12:48473800-48492800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:48474000-48493000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:48474000-48494800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:48474600-48492200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:48475000-48498200	Weak transcription	Psoas Muscle	Psoas
27	chr12:48476400-48489400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
29	chr12:48477200-48498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:48477400-48491200	Weak transcription	Fetal Kidney	kidney
31	chr12:48477400-48498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:48477800-48489400	Weak transcription	HSMM	muscle
33	chr12:48478200-48489600	Strong transcription	Fetal Muscle Leg	muscle
34	chr12:48478600-48492200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:48478600-48493600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:48478800-48489600	Strong transcription	Left Ventricle	heart
37	chr12:48478800-48489800	Strong transcription	Thymus	Thymus
38	chr12:48478800-48490200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:48478800-48492000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:48478800-48492000	Strong transcription	Liver	Liver
41	chr12:48478800-48492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:48479200-48489000	Weak transcription	Colonic Mucosa	Colon
43	chr12:48479400-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:48479400-48498200	Weak transcription	Brain Angular Gyrus	brain
45	chr12:48479400-48498400	Weak transcription	Aorta	Aorta
46	chr12:48479600-48498000	Weak transcription	NHEK	skin
47	chr12:48480000-48492800	Strong transcription	K562	blood
48	chr12:48480400-48498200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:48480800-48493600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:48481200-48493800	Strong transcription	Stomach Smooth Muscle	stomach

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