Variant report

Variant	rs2004170
Chromosome Location	chr6:76569564-76569565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10806048	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10943292	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11970551	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12209903	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12526227	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662659	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1322551	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358954	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1407510	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535501	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2181245	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2181246	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2273859	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2312940	0.88[ASN][1000 genomes]
rs2748959	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2748964	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2842538	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2842540	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2842542	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842544	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842546	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2842549	0.80[ASN][1000 genomes]
rs3798447	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3798448	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6934542	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs699186	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720862	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720863	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72890648	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9294005	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9443195	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9447579	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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

No data

Chromatin state (count:75 , 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	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:76544000-76583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:76544200-76572600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:76544400-76572600	Weak transcription	Aorta	Aorta
12	chr6:76544400-76572600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:76544400-76603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:76547400-76572600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:76551200-76572600	Weak transcription	Placenta	Placenta
16	chr6:76552000-76571200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:76552200-76572400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:76552200-76592400	Weak transcription	HSMM	muscle
19	chr6:76552600-76592400	Weak transcription	Psoas Muscle	Psoas
20	chr6:76553400-76572600	Weak transcription	Brain Angular Gyrus	brain
21	chr6:76554200-76572400	Weak transcription	Brain Substantia Nigra	brain
22	chr6:76559600-76576000	Weak transcription	Left Ventricle	heart
23	chr6:76560000-76572200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:76560000-76572600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:76560000-76585800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:76560200-76571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:76560400-76572600	Weak transcription	NH-A	brain
28	chr6:76560400-76572600	Weak transcription	NHEK	skin
29	chr6:76560400-76583200	Weak transcription	Osteobl	bone
30	chr6:76560600-76571600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:76560600-76572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:76562400-76599800	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:76562800-76569800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:76562800-76572800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:76562800-76583400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr6:76563000-76570400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:76563000-76580200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:76563000-76585400	Weak transcription	NHDF-Ad	bronchial
39	chr6:76563400-76571000	Weak transcription	HUVEC	blood vessel
40	chr6:76563400-76602800	Weak transcription	Small Intestine	intestine
41	chr6:76564400-76569600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:76564400-76570400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:76565200-76571000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:76566200-76604600	Weak transcription	Right Ventricle	heart
45	chr6:76567000-76604400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:76567400-76569600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:76567400-76570600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:76567400-76572200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:76567400-76572400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:76567400-76572800	Weak transcription	Spleen	Spleen

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