Variant report

Variant	rs12460555
Chromosome Location	chr19:40772464-40772465
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40770481..40772610-chr19:40774016..40777021,3	K562	blood:
2	chr19:40772355..40774714-chr19:40778588..40781448,2	MCF-7	breast:

Variant related genes	Relation type
AKT2	TF binding region
ENSG00000105221	Chromatin interaction
ENSG00000205041	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11083554	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12151335	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs12459567	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12977474	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12985477	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16974196	0.86[JPT][hapmap]
rs1962639	0.88[EUR][1000 genomes]
rs1991460	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2304186	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2368575	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33933140	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34894858	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs35562135	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745195	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3746006	0.86[JPT][hapmap]
rs4479364	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4490097	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4502340	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4524046	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4802072	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4802076	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4803324	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803325	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803326	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803327	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55710016	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55710849	0.82[ASN][1000 genomes]
rs57158010	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58502633	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59263025	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7259273	0.80[EUR][1000 genomes]
rs7259541	0.91[JPT][hapmap]
rs7507651	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs7508513	0.88[EUR][1000 genomes]
rs8110323	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs890773	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs892117	0.81[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer 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 miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1064502	chr19:40758049-40781360	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1063993	chr19:40763787-40781360	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1059884	chr19:40763839-40781360	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40759800-40775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:40759800-40780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:40762000-40779800	Weak transcription	Stomach Mucosa	stomach
4	chr19:40762800-40777600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:40762800-40780800	Weak transcription	Small Intestine	intestine
6	chr19:40763200-40774000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:40763600-40777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:40763800-40777600	Weak transcription	Hela-S3	cervix
9	chr19:40763800-40777600	Weak transcription	HMEC	breast
10	chr19:40765400-40777800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:40766200-40788600	Weak transcription	HSMMtube	muscle
12	chr19:40766800-40776600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:40767000-40776200	Strong transcription	Primary T cells from cord blood	blood
14	chr19:40767400-40774800	Strong transcription	Thymus	Thymus
15	chr19:40767600-40774800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:40767600-40779600	Strong transcription	Fetal Stomach	stomach
17	chr19:40767800-40780400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:40768000-40774400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:40768200-40774600	Strong transcription	Fetal Intestine Large	intestine
20	chr19:40768200-40780400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:40768400-40772600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:40769000-40772600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr19:40769000-40776600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr19:40769000-40778200	Weak transcription	HSMM	muscle
25	chr19:40769000-40779600	Strong transcription	Fetal Intestine Small	intestine
26	chr19:40769400-40773200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:40769400-40777400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:40769600-40776200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:40769600-40783600	Weak transcription	Fetal Kidney	kidney
30	chr19:40769800-40772600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:40769800-40774200	Weak transcription	NHDF-Ad	bronchial
32	chr19:40770000-40789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:40770000-40789600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:40770200-40775000	Enhancers	Brain Angular Gyrus	brain
35	chr19:40770200-40776200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:40770200-40789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
38	chr19:40770400-40772600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr19:40770400-40784000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:40770600-40774800	Enhancers	Brain Substantia Nigra	brain
41	chr19:40770600-40775000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:40770800-40772800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr19:40771000-40773000	Weak transcription	Primary B cells from cord blood	blood
44	chr19:40771000-40773200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr19:40771000-40773400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:40771000-40773400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:40771000-40774000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:40771000-40777600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:40771000-40780400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:40771000-40780800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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