Variant report

Variant	rs407226
Chromosome Location	chr3:191099647-191099648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1066857	0.96[ASN][1000 genomes]
rs13061649	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs150505	0.95[ASN][1000 genomes]
rs1656143	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662184	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167148	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1715641	0.99[ASN][1000 genomes]
rs176821	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176822	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs184140	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850961	0.89[ASN][1000 genomes]
rs186064	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs186065	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186066	0.82[EUR][1000 genomes]
rs186068	0.94[ASN][1000 genomes]
rs188384	0.80[EUR][1000 genomes]
rs211043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572064	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293800	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293802	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293804	0.81[EUR][1000 genomes]
rs293805	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293806	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293807	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293808	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293809	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293812	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293813	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293816	0.90[ASN][1000 genomes]
rs293817	0.90[ASN][1000 genomes]
rs293837	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293839	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293840	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293841	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293852	0.97[ASN][1000 genomes]
rs293854	0.97[ASN][1000 genomes]
rs293856	0.97[ASN][1000 genomes]
rs293857	0.97[ASN][1000 genomes]
rs293858	0.97[ASN][1000 genomes]
rs293859	0.95[ASN][1000 genomes]
rs293861	0.95[ASN][1000 genomes]
rs364519	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367747	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs368665	0.82[EUR][1000 genomes]
rs369174	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs381090	0.80[EUR][1000 genomes]
rs383075	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs383529	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386241	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs389765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390744	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs392311	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs399575	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs403078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420266	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs423989	0.95[ASN][1000 genomes]
rs429374	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429521	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs432085	0.82[EUR][1000 genomes]
rs434556	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs436393	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs436428	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs437244	0.81[EUR][1000 genomes]
rs438589	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs440266	0.95[ASN][1000 genomes]
rs441509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445914	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447931	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs449398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491252	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs497918	0.93[ASN][1000 genomes]
rs513632	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520494	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520600	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529523	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs566548	0.87[AFR][1000 genomes]
rs568702	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs578401	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs695910	0.89[ASN][1000 genomes]
rs696347	0.95[ASN][1000 genomes]
rs696348	0.95[ASN][1000 genomes]
rs696349	0.95[ASN][1000 genomes]
rs697905	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs697913	0.93[ASN][1000 genomes]
rs709142	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv878107	chr3:191069984-191100073	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs407226	CCDC50	cis	Artery Aorta	GTEx
rs407226	CCDC50	cis	Thyroid	GTEx
rs407226	CCDC50	cis	Artery Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
2	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:191079600-191121200	Weak transcription	Gastric	stomach
7	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
9	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:191087800-191100000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:191087800-191109200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:191088000-191109800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
17	chr3:191094600-191100600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:191094800-191102200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:191094800-191114800	Weak transcription	A549	lung
20	chr3:191095000-191100000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:191095000-191100600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:191095000-191107600	Weak transcription	Fetal Intestine Small	intestine
23	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:191096400-191101400	Strong transcription	NH-A	brain
25	chr3:191096400-191109600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:191096600-191101800	Strong transcription	Hela-S3	cervix
27	chr3:191096600-191105800	Weak transcription	Brain Substantia Nigra	brain
28	chr3:191096600-191114800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:191096800-191100000	Strong transcription	GM12878-XiMat	blood
30	chr3:191097000-191101000	Strong transcription	Placenta	Placenta
31	chr3:191097200-191100400	Strong transcription	NHDF-Ad	bronchial
32	chr3:191097200-191109200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:191097400-191099800	Strong transcription	HepG2	liver
34	chr3:191097400-191100000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:191097400-191101200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:191097400-191101400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:191097400-191101800	Strong transcription	HUVEC	blood vessel
38	chr3:191097400-191102200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:191097400-191103200	Strong transcription	Liver	Liver
40	chr3:191097400-191103400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:191097600-191100000	Weak transcription	Right Atrium	heart
42	chr3:191097600-191100400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr3:191097600-191101200	Strong transcription	NHEK	skin
44	chr3:191097600-191102600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:191097600-191103000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:191097800-191100000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:191097800-191100000	Strong transcription	HSMM	muscle
48	chr3:191097800-191101600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:191097800-191101800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:191098000-191100000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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