Variant report

Variant	rs4885356
Chromosome Location	chr13:76443405-76443406
allele	C/G
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	chr13:76443394-76443432	ProgFib	skin:	n/a	n/a
2	POLR2A	chr13:76443227-76443419	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr13:76440820-76447842	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
C13orf45	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12323251	0.87[ASN][1000 genomes]
rs12429274	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12429913	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs17715327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17716148	0.83[AMR][1000 genomes]
rs1853475	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736859	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4885352	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs4885353	1.00[CHB][hapmap]
rs56978359	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9573665	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs9573667	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs9593132	0.84[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9600559	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]

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	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4885356	SLIT1	trans	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76417400-76443800	Weak transcription	Fetal Brain Female	brain
2	chr13:76417600-76444600	Weak transcription	HMEC	breast
3	chr13:76424400-76444200	Weak transcription	Fetal Lung	lung
4	chr13:76428000-76444600	Weak transcription	Fetal Kidney	kidney
5	chr13:76428000-76444800	Weak transcription	Esophagus	oesophagus
6	chr13:76428200-76444400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:76428400-76444600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:76428400-76444600	Weak transcription	Fetal Heart	heart
9	chr13:76429600-76444600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr13:76431000-76444600	Weak transcription	Aorta	Aorta
11	chr13:76431600-76444600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:76432000-76444600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:76432200-76443600	Weak transcription	Primary T cells from cord blood	blood
14	chr13:76432200-76444200	Weak transcription	GM12878-XiMat	blood
15	chr13:76432200-76444600	Weak transcription	Fetal Intestine Small	intestine
16	chr13:76432200-76444600	Weak transcription	Fetal Muscle Leg	muscle
17	chr13:76432200-76444600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr13:76433000-76444400	Weak transcription	Liver	Liver
19	chr13:76433400-76444200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr13:76435000-76443800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:76435200-76444200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:76435600-76444400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:76436000-76444000	Weak transcription	Fetal Thymus	thymus
24	chr13:76437200-76444600	Weak transcription	HSMMtube	muscle
25	chr13:76438000-76444200	Weak transcription	NHDF-Ad	bronchial
26	chr13:76438200-76444000	Weak transcription	Hela-S3	cervix
27	chr13:76439200-76444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:76439800-76444400	Weak transcription	A549	lung
29	chr13:76440000-76443800	Weak transcription	Osteobl	bone
30	chr13:76440000-76469200	Weak transcription	HSMM	muscle
31	chr13:76442400-76444200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:76443000-76444600	Weak transcription	Ovary	ovary
33	chr13:76443200-76445400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr13:76443400-76444400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr13:76443400-76444400	Enhancers	H9 Cell Line	embryonic stem cell
36	chr13:76443400-76445000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr13:76443400-76445000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr13:76443400-76445000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr13:76443400-76445600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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