Variant report

Variant	rs12908949
Chromosome Location	chr15:59475713-59475714
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59468439..59470202-chr15:59473986..59476480,2	K562	blood:
2	chr15:59474900..59477474-chr15:59486434..59489003,2	K562	blood:

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

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

rs_ID	r²[population]
rs1032178	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1032179	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1032181	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071411	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11631844	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11633119	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11633205	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440243	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12898967	0.87[ASN][1000 genomes]
rs12912558	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12915115	0.86[ASN][1000 genomes]
rs17302219	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029212	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2171286	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242322	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2242323	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2899644	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35227552	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794496	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3794497	0.85[AMR][1000 genomes]
rs3794498	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4775120	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4775123	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775125	0.96[EUR][1000 genomes]
rs58583822	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62004105	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62004107	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7178908	0.86[ASN][1000 genomes]
rs7181609	0.89[EUR][1000 genomes]
rs8041615	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
2	chr15:59445600-59479600	Weak transcription	Fetal Kidney	kidney
3	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:59464400-59496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:59467800-59479600	Weak transcription	Brain Angular Gyrus	brain
6	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
7	chr15:59468000-59479800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:59468000-59480000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
10	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr15:59468800-59490800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr15:59468800-59492600	Strong transcription	Fetal Intestine Large	intestine
13	chr15:59469000-59482800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:59470000-59475800	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:59470000-59482200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:59470800-59485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:59471000-59480400	Weak transcription	Colonic Mucosa	Colon
18	chr15:59471000-59484000	Weak transcription	Esophagus	oesophagus
19	chr15:59471400-59480000	Weak transcription	Left Ventricle	heart
20	chr15:59471400-59482200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:59471600-59476600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:59471800-59475800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:59471800-59479400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:59471800-59479600	Weak transcription	Gastric	stomach
25	chr15:59472600-59480600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:59473000-59476200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:59473200-59477600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:59473400-59482200	Weak transcription	Spleen	Spleen
29	chr15:59473600-59479600	Weak transcription	Fetal Heart	heart
30	chr15:59473800-59475800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:59473800-59476000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr15:59473800-59477000	ZNF genes & repeats	GM12878-XiMat	blood
33	chr15:59473800-59477400	ZNF genes & repeats	A549	lung
34	chr15:59473800-59478800	Strong transcription	Osteobl	bone
35	chr15:59474000-59476800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:59474000-59476800	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr15:59474000-59477200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr15:59474000-59477400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:59474000-59483400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:59474200-59479600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:59474200-59479600	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:59474200-59479600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:59474200-59479600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:59474200-59479800	Weak transcription	Brain Substantia Nigra	brain
45	chr15:59474200-59480000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:59474400-59478000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:59474400-59480000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:59474400-59482400	Weak transcription	HepG2	liver
49	chr15:59474400-59483800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:59474400-59484600	Weak transcription	Colon Smooth Muscle	Colon

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