Variant report

Variant	rs33569
Chromosome Location	chr5:112303737-112303738
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112255892..112258001-chr5:112300959..112303737,2	MCF-7	breast:
2	chr5:112249716..112252598-chr5:112302249..112303940,2	MCF-7	breast:
3	chr5:112303578..112305254-chr5:112311850..112314177,2	MCF-7	breast:
4	chr5:112298220..112301576-chr5:112303525..112306248,4	K562	blood:
5	chr5:112295383..112297610-chr5:112302677..112305586,2	K562	blood:

Variant related genes	Relation type
ENSG00000172795	Chromatin interaction
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1057474	0.80[CHB][hapmap]
rs13156493	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs13177101	0.81[JPT][hapmap];0.85[TSI][hapmap]
rs13186334	0.80[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs13445	0.81[CHD][hapmap];0.82[TSI][hapmap]
rs1363333	0.80[CHB][hapmap]
rs1549181	0.80[CHB][hapmap]
rs17372511	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2112454	0.85[CHB][hapmap];0.82[TSI][hapmap]
rs2416300	0.83[JPT][hapmap]
rs3185733	0.80[CHB][hapmap]
rs33544	0.80[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs33551	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs33554	0.85[ASN][1000 genomes]
rs33557	0.80[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs33558	0.81[EUR][1000 genomes]
rs33559	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33560	0.86[ASN][1000 genomes]
rs33561	0.80[EUR][1000 genomes]
rs33568	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3857434	0.80[CHB][hapmap]
rs4705750	0.80[CHB][hapmap]
rs4778	0.81[JPT][hapmap]
rs7670	0.80[TSI][hapmap]
rs7701781	0.80[CHB][hapmap];0.81[TSI][hapmap]
rs9122	0.80[CHB][hapmap];0.83[MEX][hapmap]
rs9784647	0.81[JPT][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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs33569	MCC	cis	cerebellum	SCAN
rs33569	MCC	cis	Whole Blood	GTEx
rs33569	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs33569	TSLP	cis	parietal	SCAN
rs33569	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112294000-112311800	Weak transcription	Right Atrium	heart
2	chr5:112294800-112304400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:112295200-112304400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:112297000-112304400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:112298200-112311800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:112300000-112305200	Weak transcription	NH-A	brain
7	chr5:112300000-112305600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:112300000-112307000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:112300200-112303800	Weak transcription	A549	lung
10	chr5:112300200-112305000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:112300200-112305000	Weak transcription	Hela-S3	cervix
12	chr5:112300200-112305000	Weak transcription	HUVEC	blood vessel
13	chr5:112300200-112305000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr5:112300200-112311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:112300400-112303800	Weak transcription	K562	blood
16	chr5:112300400-112304200	Weak transcription	GM12878-XiMat	blood
17	chr5:112300400-112304600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:112300400-112305200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:112302000-112306200	Enhancers	Placenta	Placenta
20	chr5:112302200-112303800	Enhancers	HepG2	liver
21	chr5:112302600-112305200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:112303200-112304000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr5:112303600-112305600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:112303600-112305800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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