Variant report

Variant	rs62408893
Chromosome Location	chr3:179141837-179141838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10937003	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11539416	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11714353	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11715227	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11717019	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11720405	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12632708	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12634184	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13327561	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2111278	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287212	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287311	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28588445	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58230199	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60388496	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62408905	0.81[AFR][1000 genomes]
rs6774135	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73172210	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9790192	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
2	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
4	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:179111800-179150600	Weak transcription	Psoas Muscle	Psoas
7	chr3:179112000-179167200	Weak transcription	Fetal Kidney	kidney
8	chr3:179112200-179142600	Weak transcription	Esophagus	oesophagus
9	chr3:179112800-179144200	Weak transcription	A549	lung
10	chr3:179113800-179146800	Weak transcription	Gastric	stomach
11	chr3:179120600-179143800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:179120800-179144600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:179121000-179149400	Weak transcription	Primary T cells from cord blood	blood
14	chr3:179121400-179143000	Weak transcription	Fetal Intestine Small	intestine
15	chr3:179122400-179142000	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:179122800-179149800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:179123000-179143000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:179123000-179143200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:179123000-179150400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:179123200-179142200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:179123200-179154800	Weak transcription	Brain Anterior Caudate	brain
22	chr3:179123400-179142400	Weak transcription	Right Ventricle	heart
23	chr3:179123400-179149600	Weak transcription	Fetal Intestine Large	intestine
24	chr3:179123600-179153600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:179123800-179156400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:179125600-179142000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:179127200-179145000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:179127600-179145200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:179131600-179147400	Weak transcription	Fetal Heart	heart
30	chr3:179132800-179167000	Weak transcription	Hela-S3	cervix
31	chr3:179133000-179142600	Weak transcription	HMEC	breast
32	chr3:179133200-179149400	Weak transcription	Brain Angular Gyrus	brain
33	chr3:179133400-179150400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:179135800-179142400	Weak transcription	Fetal Thymus	thymus
35	chr3:179137200-179149000	Weak transcription	GM12878-XiMat	blood
36	chr3:179137400-179156400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:179139200-179145000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:179139800-179142000	Weak transcription	HSMMtube	muscle
39	chr3:179139800-179143600	Strong transcription	Fetal Stomach	stomach
40	chr3:179139800-179149200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:179139800-179149400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:179139800-179150400	Weak transcription	Brain Substantia Nigra	brain
43	chr3:179139800-179153200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:179140400-179145200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:179140800-179143200	Strong transcription	Primary B cells from cord blood	blood
46	chr3:179140800-179143400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:179140800-179143400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:179140800-179143800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:179140800-179144000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:179140800-179144000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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