Variant report

Variant	rs33557
Chromosome Location	chr5:112310396-112310397
allele	A/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	CTCF	chr5:112310380-112310530	GM12864	blood:	n/a	n/a
2	GATA1	chr5:112309379-112313322	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112291720..112294004-chr5:112309905..112311791,2	MCF-7	breast:
2	chr5:112308899..112310478-chr5:112310482..112312099,2	MCF-7	breast:
3	chr5:112255914..112262078-chr5:112308752..112315375,16	MCF-7	breast:
4	chr5:112255338..112258184-chr5:112308831..112311561,3	MCF-7	breast:

Variant related genes	Relation type
DCP2	TF binding region
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1057474	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs13156493	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs13177101	0.85[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs13186334	0.85[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap]
rs13445	0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap]
rs1363333	0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs1549181	0.90[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs17372511	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2112454	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs2416300	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs3185733	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs33544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33545	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33548	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33549	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33551	1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs33552	1.00[CEU][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs33554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33558	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs33559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33560	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33561	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs33566	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs33568	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33569	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]
rs3857434	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4074190	0.81[JPT][hapmap]
rs4075350	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs4301226	0.81[JPT][hapmap]
rs4705749	0.85[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap]
rs4705750	0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs4705752	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4705758	0.81[JPT][hapmap]
rs4778	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs6594665	0.81[JPT][hapmap]
rs6877769	0.81[JPT][hapmap]
rs6894219	0.81[JPT][hapmap]
rs7670	0.85[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap]
rs7701781	0.90[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9122	0.90[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs9784647	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs33557	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs33557	MCC	cis	cerebellum	SCAN
rs33557	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs33557	TSLP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112294000-112311800	Weak transcription	Right Atrium	heart
2	chr5:112298200-112311800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:112300200-112311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:112305600-112311600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:112305600-112311600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:112305600-112311600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:112305600-112311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:112305600-112311800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:112305600-112312000	Weak transcription	Hela-S3	cervix
10	chr5:112305800-112310400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:112305800-112311400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:112305800-112311600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:112305800-112311600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:112306000-112311000	Weak transcription	HepG2	liver
15	chr5:112306000-112311400	Weak transcription	A549	lung
16	chr5:112306000-112311600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:112306000-112311600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:112306000-112311800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:112307200-112311400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:112307200-112311600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:112307200-112311600	Weak transcription	Fetal Kidney	kidney
22	chr5:112307400-112311400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:112307400-112311400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:112307800-112311200	Weak transcription	GM12878-XiMat	blood
25	chr5:112307800-112311400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:112307800-112311600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:112308600-112311800	Enhancers	Placenta	Placenta
28	chr5:112309200-112311800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:112309800-112310600	Flanking Active TSS	K562	blood
30	chr5:112309800-112311600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:112309800-112312000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:112310000-112311400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:112310000-112311600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:112310000-112311600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:112310000-112311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:112310000-112312000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:112310200-112311600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:112310200-112311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:112310200-112311600	Weak transcription	Fetal Thymus	thymus

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