Variant report

Variant	rs1539438
Chromosome Location	chr1:114430356-114430357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:114430302-114430880	HCT-116	colon:	n/a	n/a
2	JUND	chr1:114429909-114430890	HCT-116	colon:	n/a	n/a
3	ELF1	chr1:114429941-114430788	HCT-116	colon:	n/a	n/a
4	FOXM1	chr1:114430273-114430894	ECC-1	luminal epithelium:	n/a	n/a
5	TEAD4	chr1:114430307-114430901	ECC-1	luminal epithelium:	n/a	n/a
6	CBX3	chr1:114429885-114430896	HCT-116	colon:	n/a	n/a
7	SIN3AK20	chr1:114430266-114430856	HCT-116	colon:	n/a	n/a
8	TEAD4	chr1:114430348-114430805	HCT-116	colon:	n/a	n/a
9	MAX	chr1:114430017-114430836	HCT-116	colon:	n/a	n/a
10	SP1	chr1:114429833-114430980	HCT-116	colon:	n/a	n/a
11	CEBPB	chr1:114429877-114430931	HCT-116	colon:	n/a	n/a
12	FOSL1	chr1:114430337-114430882	HCT-116	colon:	n/a	n/a
13	JUND	chr1:114429830-114430823	HCT-116	colon:	n/a	n/a
14	SP1	chr1:114430315-114430858	HCT-116	colon:	n/a	n/a
15	NFIC	chr1:114430339-114430929	ECC-1	luminal epithelium:	n/a	n/a
16	FOSL1	chr1:114429956-114430925	HCT-116	colon:	n/a	n/a
17	EP300	chr1:114430259-114430986	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114430286..114432860-chr1:114447096..114449526,2	K562	blood:
2	chr1:114429070..114435293-chr1:114435414..114441720,10	MCF-7	breast:

No data

Variant related genes	Relation type
BCL2L15	TF binding region
ENSG00000118655	Chromatin interaction
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10745340	0.84[CHD][hapmap]
rs10776775	0.84[CHD][hapmap]
rs1217384	1.00[ASW][hapmap]
rs1217392	0.84[CHD][hapmap]
rs1217394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12760457	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs2018365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040040	1.00[ASW][hapmap]
rs2476594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789607	1.00[ASW][hapmap]
rs3789609	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs6674848	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs6703387	1.00[ASW][hapmap];0.85[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1539438	AP4B1	cis	cerebellum	SCAN
rs1539438	CD58	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114415400-114437000	Weak transcription	Thymus	Thymus
3	chr1:114417200-114437000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:114420200-114437800	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:114420200-114446400	Weak transcription	Aorta	Aorta
6	chr1:114423600-114436000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:114424200-114437800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:114424400-114436200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:114424600-114431200	Weak transcription	Small Intestine	intestine
10	chr1:114424600-114433200	Weak transcription	GM12878-XiMat	blood
11	chr1:114424600-114436400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:114424600-114436600	Weak transcription	Fetal Thymus	thymus
13	chr1:114424600-114437800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:114424600-114438800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:114424600-114442400	Weak transcription	Psoas Muscle	Psoas
16	chr1:114425000-114436800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:114425200-114436200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:114425400-114436400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:114425400-114437400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:114425600-114436400	Weak transcription	Brain Substantia Nigra	brain
21	chr1:114426400-114431800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr1:114427200-114436800	Weak transcription	Fetal Brain Female	brain
23	chr1:114427400-114430400	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr1:114427400-114437000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:114427600-114437800	Weak transcription	Brain Angular Gyrus	brain
26	chr1:114427800-114432000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:114428200-114437000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:114428200-114437800	Weak transcription	Lung	lung
29	chr1:114428400-114430400	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:114428600-114437800	Weak transcription	Esophagus	oesophagus
31	chr1:114428800-114430400	Active TSS	Fetal Intestine Large	intestine
32	chr1:114428800-114430400	Active TSS	Fetal Intestine Small	intestine
33	chr1:114428800-114430600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:114428800-114430800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:114428800-114430800	Active TSS	Stomach Mucosa	stomach
36	chr1:114429000-114430400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:114429000-114430800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr1:114429000-114430800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:114429000-114430800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:114429200-114430400	Enhancers	Primary T cells from cord blood	blood
41	chr1:114429200-114430600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:114429200-114430800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr1:114429200-114437600	Weak transcription	HSMMtube	muscle
44	chr1:114429800-114430400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:114429800-114430600	Enhancers	K562	blood
46	chr1:114429800-114430800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:114429800-114430800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:114429800-114430800	Enhancers	NHEK	skin
49	chr1:114429800-114431200	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:114430000-114430400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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