Variant report

Variant	rs2138543
Chromosome Location	chr12:39298423-39298424
allele	A/T
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	chr12:39298240-39300998	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:39298411-39301114	GM19193	blood:	n/a	n/a
3	POLR2A	chr12:39298408-39300010	PFSK-1	brain:	n/a	n/a
4	HCFC1	chr12:39298323-39301455	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:39297427-39301143	GM12891	blood:	n/a	n/a
6	TCF12	chr12:39298349-39301042	A549	lung:	n/a	chr12:39300441-39300449 chr12:39300615-39300625
7	POLR2A	chr12:39297427-39300986	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:39298412-39299677	GM12892	blood:	n/a	n/a
9	CEBPB	chr12:39298178-39299546	A549	lung:	n/a	chr12:39298651-39298668
10	SPI1	chr12:39298421-39299209	GM12878	blood:	n/a	chr12:39298832-39298839
11	POLR2A	chr12:39298334-39300090	GM12878	blood:	n/a	n/a
12	SP1	chr12:39298402-39300969	A549	lung:	n/a	chr12:39300129-39300138 chr12:39299581-39299595 chr12:39299467-39299481 chr12:39300129-39300139 chr12:39300128-39300140 chr12:39299471-39299485 chr12:39300130-39300139 chr12:39299443-39299457 chr12:39300128-39300140
13	GTF3C2	chr12:39298033-39299322	Hela-S3	cervix:	n/a	n/a
14	STAT3	chr12:39298419-39299592	MCF10A-Er-Src	breast:	n/a	chr12:39299472-39299484 chr12:39299010-39299021 chr12:39299012-39299020 chr12:39299477-39299489 chr12:39299214-39299226 chr12:39298749-39298770 chr12:39299012-39299035 chr12:39299219-39299231 chr12:39298834-39298841
15	CEBPB	chr12:39298343-39299676	Hela-S3	cervix:	n/a	chr12:39298651-39298668
16	POLR2A	chr12:39298420-39300056	GM12891	blood:	n/a	n/a
17	PML	chr12:39298417-39301088	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:39295565..39299427-chr12:39307532..39310185,3	K562	blood:
2	chr12:39298360..39299282-chr5:99870676..99871194,2	Hela-S3	cervix:
3	chr12:39298324..39299381-chr7:141251113..141251796,3	Hela-S3	cervix:
4	chr12:39294074..39295589-chr12:39295957..39298877,2	K562	blood:

Variant related genes	Relation type
ENSG00000257718	TF binding region
ENSG00000174132	Chromatin interaction
ENSG00000247877	Chromatin interaction
ENSG00000006530	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10444553	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876208	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1400280	0.82[AMR][1000 genomes]
rs1400285	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1516558	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2388172	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56149694	0.81[AMR][1000 genomes]
rs6580849	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7962363	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7970097	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39287400-39298600	Weak transcription	Aorta	Aorta
2	chr12:39290800-39298600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:39292400-39298800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:39296200-39300200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:39297000-39299000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:39297000-39301200	Active TSS	Right Atrium	heart
7	chr12:39297200-39298600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:39297200-39301000	Active TSS	Brain Hippocampus Middle	brain
9	chr12:39297200-39301000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:39297200-39301000	Active TSS	K562	blood
11	chr12:39297200-39301200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:39297400-39298600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:39297400-39298600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:39297400-39299200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr12:39297400-39301000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr12:39297600-39298600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr12:39297600-39298600	Enhancers	Primary B cells from cord blood	blood
18	chr12:39297600-39299000	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr12:39297600-39300800	Active TSS	Brain Anterior Caudate	brain
20	chr12:39297600-39301000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:39297600-39301400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:39297600-39301400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:39297800-39298600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:39297800-39299200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:39297800-39300200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:39297800-39301000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:39297800-39301200	Active TSS	Brain Angular Gyrus	brain
28	chr12:39297800-39301200	Active TSS	Brain Cingulate Gyrus	brain
29	chr12:39297800-39301400	Active TSS	GM12878-XiMat	blood
30	chr12:39298000-39298600	Active TSS	Primary T cells from cord blood	blood
31	chr12:39298000-39298600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:39298000-39298600	Enhancers	Fetal Thymus	thymus
33	chr12:39298000-39300000	Active TSS	Osteobl	bone
34	chr12:39298000-39300200	Active TSS	NHLF	lung
35	chr12:39298000-39300800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr12:39298000-39300800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:39298000-39300800	Active TSS	Lung	lung
38	chr12:39298000-39301000	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr12:39298000-39301000	Active TSS	Duodenum Mucosa	Duodenum
40	chr12:39298000-39301200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:39298000-39301400	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr12:39298200-39298600	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr12:39298200-39298600	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr12:39298200-39299200	Active TSS	Adipose Nuclei	Adipose
45	chr12:39298200-39299600	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr12:39298200-39299600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:39298200-39299800	Active TSS	Stomach Smooth Muscle	stomach
48	chr12:39298200-39300000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:39298200-39300800	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr12:39298200-39300800	Active TSS	Rectal Smooth Muscle	rectum

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