Variant report

Variant	rs12423802
Chromosome Location	chr12:56159339-56159340
allele	A/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	chr12:56159145-56159450	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:56159125-56159460	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56159003..56161708-chr12:56163699..56166884,3	K562	blood:
2	chr12:56155018..56156725-chr12:56158057..56159644,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257509	TF binding region
SARNP	TF binding region
ENSG00000257509	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1056784	1.00[YRI][hapmap]
rs11574657	1.00[YRI][hapmap]
rs17844787	1.00[YRI][hapmap]
rs2071024	1.00[YRI][hapmap]
rs3741502	1.00[YRI][hapmap]
rs3858538	1.00[YRI][hapmap]

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	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56139400-56174600	Weak transcription	Stomach Mucosa	stomach
2	chr12:56141600-56161400	Strong transcription	Primary T cells from cord blood	blood
3	chr12:56142000-56191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:56142200-56161000	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr12:56142200-56162000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:56142400-56161400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:56142600-56161000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:56142600-56161200	Strong transcription	Dnd41	blood
9	chr12:56142600-56162000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:56143200-56161400	Strong transcription	Fetal Muscle Leg	muscle
11	chr12:56143800-56170000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:56144600-56208800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:56144800-56161200	Strong transcription	Fetal Thymus	thymus
14	chr12:56144800-56198600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr12:56145200-56160400	Strong transcription	A549	lung
16	chr12:56145200-56199400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:56146600-56161400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:56146600-56166200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:56149000-56159600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:56149400-56209600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:56150000-56167000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:56150400-56161200	Strong transcription	Hela-S3	cervix
23	chr12:56151000-56163000	Strong transcription	Fetal Intestine Small	intestine
24	chr12:56151600-56165800	Weak transcription	Fetal Heart	heart
25	chr12:56151800-56160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:56151800-56164800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:56152000-56162800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:56152000-56165800	Weak transcription	Psoas Muscle	Psoas
29	chr12:56152000-56173200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:56152400-56164800	Weak transcription	Small Intestine	intestine
31	chr12:56152600-56165600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:56152600-56171400	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:56152600-56179600	Weak transcription	Pancreas	Pancrea
34	chr12:56152800-56162600	Strong transcription	Fetal Stomach	stomach
35	chr12:56152800-56166200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:56152800-56209000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:56153000-56174600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:56153000-56176400	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:56153000-56182400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:56153200-56159400	Weak transcription	Gastric	stomach
41	chr12:56153200-56165400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:56153200-56171600	Weak transcription	Esophagus	oesophagus
43	chr12:56153400-56163200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:56153400-56175800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:56153800-56170600	Weak transcription	Ovary	ovary
46	chr12:56154000-56159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:56154000-56165200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:56154200-56159400	Weak transcription	Lung	lung
49	chr12:56154200-56159600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:56154200-56163400	Weak transcription	HMEC	breast

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