Variant report

Variant	rs13138117
Chromosome Location	chr4:79689207-79689208
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	CUX1	chr4:79688776-79689760	K562	blood:	n/a	n/a
2	GATA1	chr4:79689057-79690227	PBDE	blood:	n/a	chr4:79689397-79689410 chr4:79689399-79689406 chr4:79689398-79689408 chr4:79689399-79689408 chr4:79690093-79690102

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79686100..79693924-chr4:79694940..79698947,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239793	TF binding region
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10018189	0.95[CEU][hapmap]
rs10025599	0.95[CEU][hapmap]
rs10028067	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10034295	0.82[MEX][hapmap]
rs1061400	0.89[CHB][hapmap]
rs10857059	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1299129	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs13122868	0.89[CHB][hapmap]
rs1426138	0.89[CHB][hapmap]
rs1871706	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2162228	0.90[YRI][hapmap]
rs2288254	0.95[CEU][hapmap]
rs3822106	0.95[CEU][hapmap]
rs6811782	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6843114	0.95[LWK][hapmap];0.90[YRI][hapmap]
rs6858740	0.86[JPT][hapmap]
rs7664587	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs7688534	0.95[CEU][hapmap]
rs9307446	1.00[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803379	chr4:79661618-79704210	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1792021	chr4:79661618-79784245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13138117	LIN54	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79680800-79689600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:79684600-79689400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:79685800-79695400	Enhancers	K562	blood
4	chr4:79686000-79689600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:79686400-79689600	Weak transcription	NHEK	skin
6	chr4:79686800-79689400	Enhancers	Primary B cells from peripheral blood	blood
7	chr4:79686800-79691600	Enhancers	Fetal Intestine Large	intestine
8	chr4:79687200-79689400	Weak transcription	Fetal Heart	heart
9	chr4:79687400-79696000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:79687600-79689400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:79687600-79689800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:79687600-79696200	Weak transcription	Osteobl	bone
13	chr4:79687800-79689400	Weak transcription	NHDF-Ad	bronchial
14	chr4:79687800-79689600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:79687800-79689600	Weak transcription	Ovary	ovary
16	chr4:79688200-79689800	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr4:79688400-79690200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr4:79688600-79690800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:79688600-79691600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr4:79688600-79692000	Enhancers	Fetal Intestine Small	intestine
21	chr4:79688800-79689600	Enhancers	GM12878-XiMat	blood
22	chr4:79689000-79689400	Weak transcription	Fetal Thymus	thymus
23	chr4:79689000-79689400	Weak transcription	Thymus	Thymus
24	chr4:79689000-79691600	Enhancers	NHLF	lung
25	chr4:79689200-79689800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:79689200-79691000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:79689200-79691200	Enhancers	Dnd41	blood
28	chr4:79689200-79691600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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