Variant report

Variant	rs12023499
Chromosome Location	chr1:155031376-155031377
allele	C/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	chr1:155031315-155031406	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154971124..154975632-chr1:155030158..155034057,4	K562	blood:
2	chr1:154954995..154957333-chr1:155031077..155033071,2	MCF-7	breast:
3	chr1:155013927..155032770-chr1:155044175..155061131,53	MCF-7	breast:
4	chr1:154969072..154977664-chr1:155030052..155039846,22	MCF-7	breast:

Variant related genes	Relation type
EFNA4	TF binding region
EFNA3	TF binding region
ENSG00000251246	TF binding region
ADAM15	TF binding region
ENSG00000143590	Chromatin interaction
ENSG00000160688	Chromatin interaction
ENSG00000160685	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2306125	0.91[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs3765087	0.86[CHB][hapmap]
rs4845407	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription 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	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv872456	chr1:155028692-155035611	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers 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	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12023499	C1orf56	cis	parietal	SCAN
rs12023499	ETV3L	cis	parietal	SCAN
rs12023499	SETDB1	cis	parietal	SCAN
rs12023499	PMF1	cis	cerebellum	SCAN
rs12023499	JTB	cis	parietal	SCAN
rs12023499	UBE2Q1	cis	cerebellum	SCAN
rs12023499	OAZ3	cis	parietal	SCAN
rs12023499	OTUD7B	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155025000-155034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:155025200-155034000	Weak transcription	NH-A	brain
3	chr1:155025200-155034200	Weak transcription	Psoas Muscle	Psoas
4	chr1:155025200-155034200	Weak transcription	NHDF-Ad	bronchial
5	chr1:155025400-155034000	Weak transcription	GM12878-XiMat	blood
6	chr1:155025600-155033800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:155025600-155034200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:155025800-155031400	Strong transcription	Fetal Intestine Small	intestine
9	chr1:155025800-155031800	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr1:155025800-155033600	Strong transcription	A549	lung
11	chr1:155025800-155034000	Strong transcription	Brain Cingulate Gyrus	brain
12	chr1:155026000-155033200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:155026000-155033600	Strong transcription	Brain Substantia Nigra	brain
14	chr1:155026000-155033800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:155026000-155033800	Strong transcription	Fetal Stomach	stomach
16	chr1:155026000-155034200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:155026000-155034200	Weak transcription	Right Atrium	heart
18	chr1:155026200-155032600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:155026200-155033000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:155026200-155033200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr1:155026200-155033400	Strong transcription	HMEC	breast
22	chr1:155026200-155033600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:155026200-155033600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr1:155026200-155033800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:155026200-155033800	Weak transcription	Primary B cells from cord blood	blood
26	chr1:155026200-155033800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:155026200-155034000	Weak transcription	Fetal Lung	lung
28	chr1:155026200-155034200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:155026400-155031600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:155026400-155031600	Strong transcription	Hela-S3	cervix
31	chr1:155026400-155032600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:155026400-155033200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:155026400-155033400	Strong transcription	Gastric	stomach
34	chr1:155026400-155033400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:155026400-155033600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:155026400-155033600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:155026400-155033600	Strong transcription	Brain Anterior Caudate	brain
38	chr1:155026400-155033600	Strong transcription	Ovary	ovary
39	chr1:155026400-155033600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:155026400-155033800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:155026400-155033800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:155026400-155033800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:155026400-155034000	Strong transcription	Lung	lung
44	chr1:155026600-155032800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:155026600-155032800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:155026600-155033000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:155026600-155033200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:155026600-155033400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:155026600-155033400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:155026600-155033600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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