Variant report

Variant	rs12912558
Chromosome Location	chr15:59490726-59490727
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1032178	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1032179	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1032181	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11071411	0.84[AMR][1000 genomes]
rs11631844	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11633119	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11633205	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440243	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12908949	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12915115	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17302219	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2029212	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2171286	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242322	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2242323	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2899644	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34412930	0.80[EUR][1000 genomes]
rs35227552	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794496	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3794497	0.84[AMR][1000 genomes]
rs3794498	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4775120	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4775123	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4775125	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58583822	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62004105	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62004107	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178908	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181609	0.87[EUR][1000 genomes]
rs8041615	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59464400-59496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
3	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
4	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr15:59468800-59490800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr15:59468800-59492600	Strong transcription	Fetal Intestine Large	intestine
7	chr15:59475200-59503200	Strong transcription	Liver	Liver
8	chr15:59475800-59498200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr15:59475800-59517800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:59477000-59498000	Strong transcription	GM12878-XiMat	blood
11	chr15:59480200-59492400	Weak transcription	Fetal Heart	heart
12	chr15:59480200-59499200	Weak transcription	Fetal Lung	lung
13	chr15:59480200-59507200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:59480600-59496400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:59480600-59507600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:59481000-59492000	Strong transcription	Fetal Intestine Small	intestine
17	chr15:59481400-59496000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:59482800-59499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:59483200-59514000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:59484200-59499400	Weak transcription	Fetal Kidney	kidney
21	chr15:59485200-59491000	Strong transcription	HSMMtube	muscle
22	chr15:59485200-59492200	Strong transcription	Hela-S3	cervix
23	chr15:59485200-59492200	Strong transcription	HSMM	muscle
24	chr15:59485400-59515400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:59485600-59492000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:59485600-59492400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:59485600-59492600	Strong transcription	NHEK	skin
28	chr15:59485600-59505800	Weak transcription	Brain Germinal Matrix	brain
29	chr15:59485600-59521200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:59485800-59492200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:59486800-59494000	Weak transcription	Brain Anterior Caudate	brain
32	chr15:59487200-59494000	Weak transcription	Brain Angular Gyrus	brain
33	chr15:59487200-59494400	Weak transcription	Fetal Thymus	thymus
34	chr15:59487200-59502600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:59487400-59493800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:59487400-59494000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr15:59487600-59492200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:59487600-59492200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:59487600-59492200	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:59487600-59492600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:59487600-59494000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:59487600-59498000	Weak transcription	Right Ventricle	heart
43	chr15:59487600-59499400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:59487800-59490800	Weak transcription	Primary B cells from cord blood	blood
45	chr15:59487800-59492000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:59487800-59492000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:59487800-59492000	Weak transcription	Brain Substantia Nigra	brain
48	chr15:59487800-59492000	Weak transcription	Placenta	Placenta
49	chr15:59487800-59492000	Weak transcription	Lung	lung
50	chr15:59487800-59492000	Weak transcription	Rectal Smooth Muscle	rectum

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