Variant report

Variant	rs12025088
Chromosome Location	chr1:223931297-223931298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:223930362-223932021	U87	brain:	n/a	n/a
2	POLR2A	chr1:223930402-223931907	A549	lung:	n/a	n/a
3	POLR2A	chr1:223930267-223932010	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223907255..223908800-chr1:223930400..223932243,2	MCF-7	breast:
2	chr1:223931292..223932836-chr1:224033167..224035727,2	K562	blood:
3	chr1:223929603..223931458-chr1:223939312..223941787,2	K562	blood:
4	chr1:223903418..223905687-chr1:223928822..223931791,2	MCF-7	breast:
5	chr1:223900092..223902158-chr1:223929992..223931627,2	K562	blood:
6	chr1:223931041..223933395-chr1:223937050..223938620,2	K562	blood:
7	chr1:223908483..223912094-chr1:223930572..223933646,3	MCF-7	breast:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12022934	0.90[ASN][1000 genomes]
rs12023822	0.90[ASN][1000 genomes]
rs12037507	0.90[ASN][1000 genomes]
rs12046438	0.90[ASN][1000 genomes]
rs12048989	0.81[ASN][1000 genomes]
rs1542507	0.81[ASN][1000 genomes]
rs28370041	0.90[ASN][1000 genomes]
rs28370095	0.83[ASN][1000 genomes]
rs28370112	0.83[ASN][1000 genomes]
rs3754088	0.83[ASN][1000 genomes]
rs3767713	0.83[ASN][1000 genomes]
rs3820474	0.81[ASN][1000 genomes]
rs3820481	0.83[ASN][1000 genomes]
rs59206866	0.88[ASN][1000 genomes]
rs7538151	0.83[ASN][1000 genomes]
rs9804140	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer 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 target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:223915800-223931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:223916600-223932600	Weak transcription	Fetal Brain Female	brain
6	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:223921200-223932800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:223921200-223936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:223921400-223931400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:223921600-223932800	Weak transcription	Liver	Liver
12	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:223921800-223933400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:223921800-223935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:223921800-223936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:223922200-223934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:223922200-223935600	Weak transcription	Fetal Brain Male	brain
18	chr1:223922800-223931600	Weak transcription	Brain Germinal Matrix	brain
19	chr1:223922800-223934800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:223923000-223931800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:223925200-223934600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:223925400-223931800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:223925400-223931800	Weak transcription	Ovary	ovary
24	chr1:223925400-223934800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:223926800-223931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:223926800-223931600	Weak transcription	Hela-S3	cervix
27	chr1:223926800-223932800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:223927400-223933000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:223927600-223931600	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:223927800-223931600	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:223927800-223935400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:223928000-223931400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:223928000-223931400	Weak transcription	Brain Anterior Caudate	brain
34	chr1:223928000-223932800	Weak transcription	Esophagus	oesophagus
35	chr1:223928000-223933200	Weak transcription	Psoas Muscle	Psoas
36	chr1:223928000-223935400	Weak transcription	Small Intestine	intestine
37	chr1:223928000-223935600	Weak transcription	Right Atrium	heart
38	chr1:223928000-223936400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:223928200-223933400	Weak transcription	K562	blood
40	chr1:223928400-223936200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:223928600-223931400	Weak transcription	Brain Substantia Nigra	brain
42	chr1:223928800-223931600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:223928800-223932000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:223929000-223931800	Weak transcription	Aorta	Aorta
45	chr1:223929000-223934800	Weak transcription	Fetal Kidney	kidney
46	chr1:223929400-223931600	Enhancers	Left Ventricle	heart
47	chr1:223929400-223932200	Genic enhancers	A549	lung
48	chr1:223929800-223931800	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr1:223929800-223935200	Weak transcription	Fetal Heart	heart
50	chr1:223930000-223931800	Weak transcription	Placenta	Placenta

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