Variant report

Variant	rs62414789
Chromosome Location	chr6:76558989-76558990
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:76459743..76462264-chr6:76558072..76560658,3	MCF-7	breast:
2	chr6:76527031..76529550-chr6:76557950..76559452,2	MCF-7	breast:
3	chr6:76460418..76462531-chr6:76558690..76560910,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196586	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10498904	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11751588	0.80[ASN][1000 genomes]
rs11752694	0.86[ASN][1000 genomes]
rs11753849	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11754663	0.86[ASN][1000 genomes]
rs11755704	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11756209	0.86[ASN][1000 genomes]
rs11758543	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758976	0.86[ASN][1000 genomes]
rs11759036	0.86[ASN][1000 genomes]
rs12606	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12664049	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1280038	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1280040	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17189990	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17191306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17192223	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17192279	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17414687	0.86[ASN][1000 genomes]
rs17414729	0.86[ASN][1000 genomes]
rs17414757	0.86[ASN][1000 genomes]
rs17499531	0.86[ASN][1000 genomes]
rs17792195	0.86[ASN][1000 genomes]
rs17792285	0.86[ASN][1000 genomes]
rs17792478	0.80[ASN][1000 genomes]
rs17794529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17800625	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2104203	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2133193	0.86[ASN][1000 genomes]
rs2295936	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2748957	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2748960	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2748963	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2748966	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs276695	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842541	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842543	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842545	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842547	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765140	0.86[ASN][1000 genomes]
rs3798425	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3798433	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3798434	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798435	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818310	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56006932	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56173875	0.83[ASN][1000 genomes]
rs57920948	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61237402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414763	0.97[ASN][1000 genomes]
rs62414769	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62414787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414791	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414798	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414800	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414802	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414803	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414804	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62414824	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62415593	0.86[ASN][1000 genomes]
rs62415595	0.80[ASN][1000 genomes]
rs62415599	0.86[ASN][1000 genomes]
rs62415601	0.86[ASN][1000 genomes]
rs66846373	0.86[ASN][1000 genomes]
rs66926998	0.86[ASN][1000 genomes]
rs67573572	0.86[ASN][1000 genomes]
rs6912963	0.86[ASN][1000 genomes]
rs6936085	0.86[ASN][1000 genomes]
rs72886897	0.86[ASN][1000 genomes]
rs72888734	0.86[ASN][1000 genomes]
rs72888748	0.83[ASN][1000 genomes]
rs72890660	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741113	0.86[ASN][1000 genomes]
rs7748145	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7761004	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7762917	0.83[ASN][1000 genomes]
rs7773977	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7775832	0.86[ASN][1000 genomes]
rs9250	0.86[ASN][1000 genomes]
rs999209	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62414789	SENP6	cis	Whole Blood	GTEx
rs62414789	SENP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76520200-76576400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:76521800-76571000	Weak transcription	Gastric	stomach
3	chr6:76522600-76559000	Weak transcription	Fetal Kidney	kidney
4	chr6:76523800-76569000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:76533200-76559400	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:76534200-76572400	Weak transcription	Brain Anterior Caudate	brain
7	chr6:76538200-76559200	Weak transcription	Pancreas	Pancrea
8	chr6:76539400-76572400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:76541000-76590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:76541200-76572600	Weak transcription	HSMMtube	muscle
11	chr6:76541400-76559200	Weak transcription	Osteobl	bone
12	chr6:76541400-76572400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:76541600-76559400	Weak transcription	NH-A	brain
14	chr6:76543000-76568800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:76543000-76569200	Weak transcription	Lung	lung
16	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:76543200-76566600	Weak transcription	HMEC	breast
18	chr6:76543800-76559400	Weak transcription	NHDF-Ad	bronchial
19	chr6:76544000-76583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:76544200-76572600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:76544400-76559200	Weak transcription	Fetal Stomach	stomach
22	chr6:76544400-76572600	Weak transcription	Aorta	Aorta
23	chr6:76544400-76572600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:76544400-76603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:76545800-76566800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:76547400-76562400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr6:76547400-76572600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:76551000-76565600	Weak transcription	Liver	Liver
29	chr6:76551200-76566800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:76551200-76567200	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:76551200-76572600	Weak transcription	Placenta	Placenta
32	chr6:76551400-76559000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:76552000-76566800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:76552000-76571200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:76552200-76560000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:76552200-76562000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:76552200-76562000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:76552200-76567400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:76552200-76569000	Weak transcription	Adipose Nuclei	Adipose
40	chr6:76552200-76572400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:76552200-76592400	Weak transcription	HSMM	muscle
42	chr6:76552600-76592400	Weak transcription	Psoas Muscle	Psoas
43	chr6:76552800-76559000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:76553000-76559400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:76553200-76564800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:76553400-76572600	Weak transcription	Brain Angular Gyrus	brain
47	chr6:76554200-76572400	Weak transcription	Brain Substantia Nigra	brain
48	chr6:76555600-76562400	Weak transcription	Fetal Intestine Small	intestine
49	chr6:76557400-76562200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:76558000-76559000	Enhancers	HUVEC	blood vessel

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