Variant report

Variant	rs62004105
Chromosome Location	chr15:59461471-59461472
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:29)

rs_ID	r²[population]
rs1032178	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1032179	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1032181	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11071411	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631844	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11633119	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11633205	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12440243	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12908949	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912558	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12915115	0.80[ASN][1000 genomes]
rs17302219	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2029212	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2171286	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2242322	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2242323	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899644	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35227552	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794496	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794497	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3794498	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775120	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4775123	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775125	0.92[EUR][1000 genomes]
rs58583822	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62004107	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178908	0.80[ASN][1000 genomes]
rs7181609	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8041615	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59398000-59462000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:59431800-59467200	Weak transcription	Fetal Brain Female	brain
3	chr15:59432000-59465600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:59434200-59467000	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr15:59436000-59473000	Weak transcription	Brain Germinal Matrix	brain
6	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
7	chr15:59443200-59462600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:59443400-59461800	Weak transcription	Thymus	Thymus
9	chr15:59443400-59462400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:59445600-59479600	Weak transcription	Fetal Kidney	kidney
11	chr15:59445800-59462000	Weak transcription	Stomach Mucosa	stomach
12	chr15:59445800-59467000	Weak transcription	Fetal Heart	heart
13	chr15:59447000-59463600	Weak transcription	Primary B cells from cord blood	blood
14	chr15:59451200-59462600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:59451200-59473600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:59451400-59470400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:59451600-59463200	Weak transcription	Small Intestine	intestine
18	chr15:59451600-59474600	Weak transcription	Psoas Muscle	Psoas
19	chr15:59451800-59462600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:59451800-59464600	Weak transcription	Brain Angular Gyrus	brain
21	chr15:59451800-59466000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:59453400-59467200	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:59453600-59462000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:59453800-59461800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:59453800-59461800	Weak transcription	Colonic Mucosa	Colon
26	chr15:59453800-59462000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:59453800-59470000	Weak transcription	Right Ventricle	heart
28	chr15:59454000-59462000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:59454000-59462200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:59454000-59462400	Weak transcription	Lung	lung
31	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:59454400-59462400	Weak transcription	Brain Anterior Caudate	brain
33	chr15:59454800-59471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:59455200-59467200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:59455400-59462600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:59457400-59462600	Weak transcription	Fetal Thymus	thymus
37	chr15:59457800-59461800	Weak transcription	Adipose Nuclei	Adipose
38	chr15:59457800-59462400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:59458000-59462600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:59458000-59470000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:59458200-59461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:59458400-59463600	Enhancers	HUVEC	blood vessel
43	chr15:59458600-59462400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:59458600-59462600	Weak transcription	Gastric	stomach
45	chr15:59458600-59473800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr15:59459000-59464800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:59459200-59462200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:59459200-59466800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr15:59459400-59462000	Weak transcription	Pancreas	Pancrea
50	chr15:59459400-59462400	Weak transcription	Fetal Stomach	stomach

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