Variant report

Variant	rs62246130
Chromosome Location	chr3:46425202-46425203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17141006	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17141010	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17141081	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1799864	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1800024	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894389	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34138562	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35728689	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3918357	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3918363	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3918364	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62242983	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62242995	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62246129	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246140	0.86[ASN][1000 genomes]
rs62246142	0.86[ASN][1000 genomes]
rs7615686	0.87[ASN][1000 genomes]
rs7632215	0.83[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2756988	chr3:46419634-46444794	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2759146	chr3:46419634-46444794	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv10267	chr3:46423130-46440713	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46420400-46425400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:46420400-46427600	Weak transcription	Pancreas	Pancrea
3	chr3:46421400-46426000	Enhancers	Fetal Lung	lung
4	chr3:46422200-46425400	Enhancers	Stomach Mucosa	stomach
5	chr3:46422200-46435200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:46422400-46425400	Weak transcription	Thymus	Thymus
7	chr3:46422400-46426400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:46422400-46427800	Weak transcription	Esophagus	oesophagus
9	chr3:46422400-46438600	Weak transcription	Psoas Muscle	Psoas
10	chr3:46422600-46427600	Weak transcription	Hela-S3	cervix
11	chr3:46422600-46435200	Weak transcription	Right Atrium	heart
12	chr3:46422800-46429400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:46423000-46426400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:46423000-46427600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:46423000-46427600	Weak transcription	HSMM	muscle
16	chr3:46423000-46427600	Weak transcription	HSMMtube	muscle
17	chr3:46423400-46425800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:46423400-46427400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:46423800-46427400	Weak transcription	NHEK	skin
20	chr3:46424200-46425400	Enhancers	Primary B cells from cord blood	blood
21	chr3:46424200-46425800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr3:46424400-46425800	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:46424400-46425800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr3:46424400-46426800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:46424400-46427600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:46424400-46428200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:46424400-46428200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:46424400-46428200	Enhancers	Fetal Thymus	thymus
29	chr3:46424400-46428800	Enhancers	Primary hematopoietic stem cells	blood
30	chr3:46424600-46425400	Enhancers	Placenta	Placenta
31	chr3:46424600-46425400	Enhancers	Small Intestine	intestine
32	chr3:46424600-46425600	Enhancers	Adipose Nuclei	Adipose
33	chr3:46424600-46425600	Enhancers	Brain Angular Gyrus	brain
34	chr3:46424600-46425800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:46424600-46425800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr3:46424600-46426400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:46424800-46425400	Enhancers	Brain Germinal Matrix	brain
38	chr3:46424800-46425800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:46424800-46425800	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:46424800-46425800	Flanking Active TSS	Dnd41	blood
41	chr3:46424800-46425800	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr3:46424800-46426000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:46424800-46426000	Enhancers	HMEC	breast
44	chr3:46424800-46426200	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr3:46424800-46426200	Enhancers	Brain Hippocampus Middle	brain
46	chr3:46424800-46426800	Weak transcription	Fetal Intestine Small	intestine
47	chr3:46425000-46425400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:46425000-46425400	Flanking Active TSS	GM12878-XiMat	blood
49	chr3:46425000-46425600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:46425000-46425600	Enhancers	Brain Substantia Nigra	brain

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