Variant report

Variant	rs12743272
Chromosome Location	chr1:155033334-155033335
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:6)
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	ZNF263	chr1:155033312-155034383	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr1:155033275-155034855	HL-60	blood:	n/a	n/a
3	CTCF	chr1:155033240-155033390	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154941423..154943081-chr1:155031851..155033563,2	K562	blood:
2	chr1:154908713..154910557-chr1:155032303..155034913,2	MCF-7	breast:
3	chr1:154971124..154975632-chr1:155030158..155034057,4	K562	blood:
4	chr1:154927481..154932587-chr1:155031885..155037682,6	MCF-7	breast:
5	chr1:154932754..154935795-chr1:155033186..155037944,5	MCF-7	breast:
6	chr1:154969072..154977664-chr1:155030052..155039846,22	MCF-7	breast:

No data

Variant related genes	Relation type
EFNA3	TF binding region
ADAM15	TF binding region
EFNA4	TF binding region
ENSG00000251246	TF binding region
ENSG00000160691	Chromatin interaction
ENSG00000163346	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000271380	Chromatin interaction
ENSG00000163344	Chromatin interaction
ENSG00000163348	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11264305	1.00[ASN][1000 genomes]
rs17723260	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34522020	1.00[ASN][1000 genomes]
rs3765087	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845407	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4971092	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs6427184	0.93[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12743272	RXFP4	cis	parietal	SCAN
rs12743272	C1orf56	cis	parietal	SCAN
rs12743272	C1orf54	cis	cerebellum	SCAN
rs12743272	APOA1BP	cis	cerebellum	SCAN
rs12743272	ARHGEF11	cis	parietal	SCAN
rs12743272	TPM3	cis	parietal	SCAN
rs12743272	S100A3	cis	parietal	SCAN
rs12743272	SMCP	cis	cerebellum	SCAN
rs12743272	TDRKH	cis	cerebellum	SCAN

Chromatin state (count:112 , 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	chr1:155025800-155033600	Strong transcription	A549	lung
9	chr1:155025800-155034000	Strong transcription	Brain Cingulate Gyrus	brain
10	chr1:155026000-155033600	Strong transcription	Brain Substantia Nigra	brain
11	chr1:155026000-155033800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:155026000-155033800	Strong transcription	Fetal Stomach	stomach
13	chr1:155026000-155034200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:155026000-155034200	Weak transcription	Right Atrium	heart
15	chr1:155026200-155033400	Strong transcription	HMEC	breast
16	chr1:155026200-155033600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:155026200-155033600	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr1:155026200-155033800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:155026200-155033800	Weak transcription	Primary B cells from cord blood	blood
20	chr1:155026200-155033800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:155026200-155034000	Weak transcription	Fetal Lung	lung
22	chr1:155026200-155034200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:155026400-155033400	Strong transcription	Gastric	stomach
24	chr1:155026400-155033400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:155026400-155033600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:155026400-155033600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:155026400-155033600	Strong transcription	Brain Anterior Caudate	brain
28	chr1:155026400-155033600	Strong transcription	Ovary	ovary
29	chr1:155026400-155033600	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:155026400-155033800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:155026400-155033800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:155026400-155033800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:155026400-155034000	Strong transcription	Lung	lung
34	chr1:155026600-155033400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:155026600-155033400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:155026600-155033600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:155026600-155033800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:155026600-155033800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:155026600-155033800	Strong transcription	Brain Hippocampus Middle	brain
40	chr1:155026600-155033800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:155026600-155033800	Strong transcription	NHEK	skin
42	chr1:155026800-155033400	Strong transcription	Adipose Nuclei	Adipose
43	chr1:155026800-155033400	Strong transcription	Left Ventricle	heart
44	chr1:155026800-155033400	Strong transcription	Spleen	Spleen
45	chr1:155026800-155033600	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:155026800-155033800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:155026800-155034200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:155027000-155033400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:155027000-155033800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:155027800-155033600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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