Variant report

Variant	rs62414798
Chromosome Location	chr6:76586058-76586059
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10498904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753849	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12606	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664049	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1280038	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1280040	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17189990	0.83[ASN][1000 genomes]
rs17191306	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17192223	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17192279	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17794529	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17800625	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104203	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295936	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748957	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748960	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748963	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748966	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs276695	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842541	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842543	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842545	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842547	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3798425	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3798433	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3798434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818310	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006932	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57920948	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61237402	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414763	0.83[ASN][1000 genomes]
rs62414769	0.81[ASN][1000 genomes]
rs62414787	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414789	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414800	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414802	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414803	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414804	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414824	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72890660	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7748145	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7761004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773977	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs999209	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS 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 target site	40 gene(s)	inside rSNPs	diseases
4	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62414798	SENP6	cis	Whole Blood	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76541000-76590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:76544400-76603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:76552200-76592400	Weak transcription	HSMM	muscle
5	chr6:76552600-76592400	Weak transcription	Psoas Muscle	Psoas
6	chr6:76562400-76599800	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:76563400-76602800	Weak transcription	Small Intestine	intestine
8	chr6:76566200-76604600	Weak transcription	Right Ventricle	heart
9	chr6:76567000-76604400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:76567600-76598600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:76567600-76604200	Weak transcription	NHLF	lung
12	chr6:76571200-76592400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:76573000-76597800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:76573000-76624000	Weak transcription	Placenta	Placenta
15	chr6:76573200-76604200	Weak transcription	Colonic Mucosa	Colon
16	chr6:76573400-76592800	Weak transcription	Stomach Mucosa	stomach
17	chr6:76573600-76606200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:76573800-76607200	Weak transcription	Gastric	stomach
19	chr6:76573800-76608400	Weak transcription	Esophagus	oesophagus
20	chr6:76574400-76632600	Weak transcription	Spleen	Spleen
21	chr6:76575600-76586400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:76576000-76604000	Weak transcription	Fetal Brain Female	brain
23	chr6:76577200-76624600	Weak transcription	Fetal Kidney	kidney
24	chr6:76577400-76587800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:76577400-76591800	Weak transcription	NHEK	skin
26	chr6:76577400-76592000	Weak transcription	HMEC	breast
27	chr6:76577400-76594000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:76580000-76591600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:76580200-76586600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:76580600-76591800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:76581000-76594800	Strong transcription	Fetal Intestine Large	intestine
32	chr6:76582000-76593200	Weak transcription	Fetal Brain Male	brain
33	chr6:76582200-76586400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:76582600-76586400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:76582800-76586400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:76582800-76586400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:76583200-76586600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:76583200-76587600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:76583200-76589200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr6:76583400-76586200	Strong transcription	Liver	Liver
41	chr6:76583400-76586200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr6:76583400-76606200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr6:76583600-76592200	Weak transcription	Osteobl	bone
44	chr6:76583800-76603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:76583800-76624600	Weak transcription	Pancreas	Pancrea
46	chr6:76584000-76605600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:76584200-76589800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:76584200-76608400	Weak transcription	Aorta	Aorta
49	chr6:76584200-76629400	Weak transcription	Ovary	ovary
50	chr6:76584400-76590600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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