Variant report

Variant	rs2539990
Chromosome Location	chr2:63170185-63170186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13410889	0.87[ASN][1000 genomes]
rs1468748	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17027429	0.81[AFR][1000 genomes]
rs2430386	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2539978	0.83[ASN][1000 genomes]
rs2539981	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2539982	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2539984	0.85[ASN][1000 genomes]
rs2710637	0.86[ASN][1000 genomes]
rs2710639	0.81[ASN][1000 genomes]
rs2710640	0.81[AFR][1000 genomes]
rs2710647	0.84[EUR][1000 genomes]
rs2710651	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545971	0.82[AFR][1000 genomes]
rs6545972	0.81[AFR][1000 genomes]
rs7567923	0.81[AFR][1000 genomes]
rs7591708	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh 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	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63142400-63190800	Weak transcription	Brain Angular Gyrus	brain
2	chr2:63150600-63176000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:63151200-63171200	Weak transcription	Ovary	ovary
4	chr2:63151200-63175600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:63151200-63182800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:63151400-63171400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:63151400-63194200	Weak transcription	Esophagus	oesophagus
8	chr2:63151400-63194200	Weak transcription	Fetal Brain Male	brain
9	chr2:63151400-63200800	Weak transcription	Fetal Stomach	stomach
10	chr2:63151400-63208800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:63152200-63175600	Weak transcription	Primary T cells from cord blood	blood
13	chr2:63154400-63209000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:63155400-63209000	Weak transcription	Psoas Muscle	Psoas
15	chr2:63157400-63175600	Weak transcription	Left Ventricle	heart
16	chr2:63157400-63188800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:63157400-63207400	Weak transcription	Pancreas	Pancrea
18	chr2:63160200-63190000	Weak transcription	Primary B cells from cord blood	blood
19	chr2:63161800-63171200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:63161800-63184400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:63162000-63196800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:63162000-63199800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:63163000-63170800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:63165000-63171600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:63165200-63209200	Weak transcription	Aorta	Aorta
26	chr2:63167000-63194000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:63167400-63170600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:63167400-63175400	Weak transcription	NH-A	brain
29	chr2:63167400-63200800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:63167400-63206400	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:63167600-63170400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:63167600-63171600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:63167600-63173600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:63167600-63174000	Weak transcription	HSMM	muscle
35	chr2:63167600-63181800	Weak transcription	HMEC	breast
36	chr2:63167600-63187400	Weak transcription	NHLF	lung
37	chr2:63167600-63206200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
39	chr2:63167800-63170600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:63167800-63170600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:63167800-63173600	Weak transcription	NHEK	skin
42	chr2:63167800-63175400	Weak transcription	Osteobl	bone
43	chr2:63167800-63225800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:63168200-63170600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:63168200-63220200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:63168400-63171200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:63168400-63182600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:63168400-63187600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:63168600-63170600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:63168800-63170800	Weak transcription	Adipose Nuclei	Adipose

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