Variant report

Variant	rs3798488
Chromosome Location	chr6:100904105-100904106
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1506080	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17060614	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17060615	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1857859	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs241812	0.86[EUR][1000 genomes]
rs3213541	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734353	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3778030	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778032	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798490	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798492	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798495	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798497	0.87[ASN][1000 genomes]
rs3830139	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs767933	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7741057	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757905	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390379	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][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	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv515895	chr6:100868779-100910798	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
6	nsv533053	chr6:100883636-100911512	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
7	esv3435008	chr6:100903932-100904116	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100897400-100908600	Weak transcription	HSMMtube	muscle
2	chr6:100898000-100906000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:100901600-100906800	ZNF genes & repeats	Spleen	Spleen
4	chr6:100901600-100907200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:100901800-100907600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:100902000-100904400	Bivalent Enhancer	Brain Hippocampus Middle	brain
7	chr6:100902000-100913600	Active TSS	Psoas Muscle	Psoas
8	chr6:100903000-100904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:100903200-100904200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:100903200-100904200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr6:100903200-100904400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:100903200-100904400	Bivalent Enhancer	HUVEC	blood vessel
13	chr6:100903200-100904600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:100903200-100905000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr6:100903200-100906000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:100903400-100904200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:100903400-100904200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:100903400-100904200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:100903400-100904200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
20	chr6:100903400-100904200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
21	chr6:100903400-100904600	Bivalent Enhancer	Brain Germinal Matrix	brain
22	chr6:100903600-100904200	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr6:100903600-100904400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr6:100903600-100904400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:100903600-100904400	Bivalent/Poised TSS	Colonic Mucosa	Colon
26	chr6:100903600-100904400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
27	chr6:100903600-100905200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:100903800-100904200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:100903800-100904200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:100903800-100904200	Bivalent Enhancer	Colon Smooth Muscle	Colon
31	chr6:100903800-100904200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
32	chr6:100904000-100904200	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
33	chr6:100904000-100904200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr6:100904000-100904200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:100904000-100904200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:100904000-100904200	Flanking Bivalent TSS/Enh	Liver	Liver
37	chr6:100904000-100904200	Bivalent Enhancer	Fetal Stomach	stomach
38	chr6:100904000-100904200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
39	chr6:100904000-100904200	Bivalent Enhancer	Small Intestine	intestine
40	chr6:100904000-100904400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
41	chr6:100904000-100904400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:100904000-100904400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
43	chr6:100904000-100904400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:100904000-100904400	Bivalent Enhancer	Adipose Nuclei	Adipose
45	chr6:100904000-100904400	Bivalent Enhancer	Fetal Intestine Small	intestine
46	chr6:100904000-100904400	Bivalent/Poised TSS	Fetal Kidney	kidney
47	chr6:100904000-100904400	Flanking Active TSS	Pancreas	Pancrea
48	chr6:100904000-100904400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle

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