Variant report

Variant	rs1980748
Chromosome Location	chr6:118241752-118241753
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10457323	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10457324	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10499084	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1160428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203409	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1323100	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1323101	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1338975	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1361288	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1416416	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1416418	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1416419	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1416420	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1416421	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1416422	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1570447	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1998458	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2139048	0.85[AMR][1000 genomes]
rs2211098	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2224707	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2355792	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2760240	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2789010	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2789013	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4946304	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6568991	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6903073	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6935834	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6937496	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7775647	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs912088	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9320624	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9372488	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9374685	0.85[AMR][1000 genomes]
rs9374691	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9385024	0.87[AMR][1000 genomes]
rs9387517	0.85[AMR][1000 genomes]
rs9387518	0.85[AMR][1000 genomes]
rs9387531	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9398465	0.85[AMR][1000 genomes]
rs9398468	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs959714	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs982647	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118240400-118241800	Active TSS	Brain Cingulate Gyrus	brain
2	chr6:118240600-118241800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
3	chr6:118240800-118241800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:118240800-118241800	Active TSS	Brain Anterior Caudate	brain
5	chr6:118240800-118241800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:118240800-118242000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:118240800-118242200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:118240800-118242200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:118240800-118242200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:118241000-118241800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:118241000-118241800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:118241000-118241800	Active TSS	Brain Substantia Nigra	brain
13	chr6:118241000-118241800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr6:118241000-118241800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
15	chr6:118241000-118241800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr6:118241000-118241800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
17	chr6:118241000-118242000	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr6:118241000-118242000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr6:118241000-118242000	Enhancers	Liver	Liver
20	chr6:118241000-118242000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr6:118241200-118241800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:118241200-118241800	Active TSS	H1 Cell Line	embryonic stem cell
23	chr6:118241200-118241800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:118241200-118241800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:118241200-118241800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:118241200-118241800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:118241200-118241800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:118241200-118241800	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr6:118241200-118241800	Active TSS	Aorta	Aorta
30	chr6:118241200-118241800	Active TSS	Brain Angular Gyrus	brain
31	chr6:118241200-118242000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:118241200-118242000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:118241400-118241800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:118241400-118241800	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr6:118241400-118241800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:118241400-118241800	Bivalent/Poised TSS	Fetal Kidney	kidney
37	chr6:118241400-118241800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
38	chr6:118241400-118241800	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr6:118241400-118241800	Enhancers	Gastric	stomach
40	chr6:118241400-118241800	Active TSS	Pancreas	Pancrea
41	chr6:118241400-118241800	Active TSS	Psoas Muscle	Psoas
42	chr6:118241400-118241800	Bivalent/Poised TSS	NH-A	brain
43	chr6:118241400-118242000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:118241400-118242000	Flanking Bivalent TSS/Enh	HepG2	liver
45	chr6:118241400-118242600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:118241600-118241800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:118241600-118241800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
48	chr6:118241600-118241800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
49	chr6:118241600-118241800	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr6:118241600-118241800	Bivalent Enhancer	Colon Smooth Muscle	Colon

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