Variant report

Variant	rs12296400
Chromosome Location	chr12:123004586-123004587
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	chr12:123004485-123004724	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:123004039-123004715	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:123003204-123005678	K562	blood:	n/a	n/a
4	POLR2A	chr12:123003270-123005760	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:123004038-123004753	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:123003970-123004898	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:123004189-123004693	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:123004038-123004623	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:123004546-123004665	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:123004061-123004883	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr12:123003674-123004794	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr12:123004054-123004731	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr12:123004158-123004709	K562	blood:	n/a	n/a

Variant related genes	Relation type
RSRC2	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11058290	1.00[AMR][1000 genomes]
rs11058435	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12312757	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314100	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13377981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7133070	0.83[AMR][1000 genomes]
rs7294365	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7299845	0.83[AMR][1000 genomes]
rs7961579	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7969173	0.83[AMR][1000 genomes]
rs7974085	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7978870	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122986200-123007600	Weak transcription	Right Atrium	heart
2	chr12:122986400-123007800	Strong transcription	Placenta	Placenta
3	chr12:122986800-123006600	Strong transcription	Brain Germinal Matrix	brain
4	chr12:122986800-123006800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:122986800-123007000	Strong transcription	Fetal Muscle Leg	muscle
6	chr12:122986800-123009400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr12:122987000-123007800	Strong transcription	Fetal Thymus	thymus
8	chr12:122987400-123006800	Strong transcription	Duodenum Mucosa	Duodenum
9	chr12:122987400-123007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:122987400-123007200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:122987400-123007400	Strong transcription	Thymus	Thymus
12	chr12:122987400-123007600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr12:122987400-123007800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:122987400-123007800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:122987600-123004600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:122987600-123006000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:122987600-123006400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:122987600-123006400	Strong transcription	Liver	Liver
19	chr12:122987600-123006400	Strong transcription	Brain Hippocampus Middle	brain
20	chr12:122987600-123006600	Strong transcription	Primary T cells from cord blood	blood
21	chr12:122987600-123006800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:122987600-123007000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:122987600-123007000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:122987600-123007000	Strong transcription	Fetal Intestine Large	intestine
25	chr12:122987600-123007000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:122987600-123007600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:122987600-123007600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:122987600-123008000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:122987800-123004600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:122987800-123004600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:122987800-123005600	Strong transcription	Pancreas	Pancrea
32	chr12:122987800-123005600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:122987800-123006400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:122987800-123006400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr12:122987800-123006400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:122987800-123006400	Strong transcription	Adipose Nuclei	Adipose
37	chr12:122987800-123006400	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr12:122987800-123006400	Strong transcription	Colon Smooth Muscle	Colon
39	chr12:122987800-123006400	Strong transcription	Rectal Smooth Muscle	rectum
40	chr12:122987800-123006400	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:122987800-123006400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr12:122987800-123006600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:122987800-123006600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:122987800-123006600	Strong transcription	Brain Anterior Caudate	brain
45	chr12:122987800-123006600	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr12:122987800-123006600	Strong transcription	HMEC	breast
47	chr12:122987800-123006800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr12:122987800-123006800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:122987800-123006800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:122987800-123007000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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