Variant report

Variant	rs7773977
Chromosome Location	chr6:76569177-76569178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10498904	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11753849	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11755704	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11758543	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12606	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12664049	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1280038	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1280040	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17191306	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17192223	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17192279	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17794529	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17800625	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2104203	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2295936	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2748957	0.82[AMR][1000 genomes]
rs2748963	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2748966	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs276695	0.82[AMR][1000 genomes]
rs2842541	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2842543	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2842545	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2842547	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3798425	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3798433	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3798434	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3798435	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3818310	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56006932	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57920948	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61237402	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62414787	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62414789	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62414791	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62414798	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62414800	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62414802	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62414803	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62414804	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62414824	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6912861	0.82[AFR][1000 genomes]
rs72890660	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7748145	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761004	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs999209	0.91[AMR][1000 genomes];0.90[EUR][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
rs7773977	SENP6	cis	Whole Blood	GTEx
rs7773977	SENP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 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	chr6:76534200-76572400	Weak transcription	Brain Anterior Caudate	brain
4	chr6:76539400-76572400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:76541000-76590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:76541200-76572600	Weak transcription	HSMMtube	muscle
7	chr6:76541400-76572400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:76543000-76569200	Weak transcription	Lung	lung
9	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:76544000-76583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:76544200-76572600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:76544400-76572600	Weak transcription	Aorta	Aorta
13	chr6:76544400-76572600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:76544400-76603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:76547400-76572600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:76551200-76572600	Weak transcription	Placenta	Placenta
17	chr6:76552000-76571200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:76552200-76572400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:76552200-76592400	Weak transcription	HSMM	muscle
20	chr6:76552600-76592400	Weak transcription	Psoas Muscle	Psoas
21	chr6:76553400-76572600	Weak transcription	Brain Angular Gyrus	brain
22	chr6:76554200-76572400	Weak transcription	Brain Substantia Nigra	brain
23	chr6:76559600-76576000	Weak transcription	Left Ventricle	heart
24	chr6:76560000-76572200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:76560000-76572600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:76560000-76585800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:76560200-76571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:76560400-76572600	Weak transcription	NH-A	brain
29	chr6:76560400-76572600	Weak transcription	NHEK	skin
30	chr6:76560400-76583200	Weak transcription	Osteobl	bone
31	chr6:76560600-76571600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:76560600-76572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:76562400-76599800	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:76562800-76569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:76562800-76569800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:76562800-76572800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:76562800-76583400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:76563000-76570400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:76563000-76580200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:76563000-76585400	Weak transcription	NHDF-Ad	bronchial
41	chr6:76563400-76571000	Weak transcription	HUVEC	blood vessel
42	chr6:76563400-76602800	Weak transcription	Small Intestine	intestine
43	chr6:76564400-76569600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:76564400-76570400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:76565200-76571000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:76566200-76604600	Weak transcription	Right Ventricle	heart
47	chr6:76567000-76569200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:76567000-76604400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:76567400-76569600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:76567400-76570600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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