Variant report

Variant	rs33553
Chromosome Location	chr5:112314453-112314454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112202949..112204762-chr5:112314290..112317071,2	MCF-7	breast:
2	chr5:112255209..112259355-chr5:112310614..112316433,9	K562	blood:
3	chr5:112253961..112259306-chr5:112310933..112315767,8	K562	blood:
4	chr5:112313991..112316155-chr5:112326453..112328052,2	K562	blood:
5	chr5:112312938..112314772-chr5:112369842..112371988,2	K562	blood:
6	chr5:112255914..112262078-chr5:112308752..112315375,16	MCF-7	breast:
7	chr5:112312686..112316155-chr5:112325860..112328052,3	K562	blood:
8	chr5:112296171..112299064-chr5:112312877..112315865,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10059599	0.94[JPT][hapmap]
rs12516502	0.94[JPT][hapmap]
rs12719155	0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2052484	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2080896	0.94[JPT][hapmap]
rs2112452	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2112453	0.94[JPT][hapmap]
rs33543	0.80[AMR][1000 genomes]
rs33547	0.89[ASN][1000 genomes]
rs33550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs33556	0.82[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33562	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs33563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs33567	0.88[YRI][hapmap]
rs3733969	0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3857433	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4260660	0.88[JPT][hapmap]
rs4705530	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4705533	0.94[JPT][hapmap]
rs4705743	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4705746	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs4705754	0.93[JPT][hapmap]
rs6594659	0.88[JPT][hapmap]
rs7447818	0.94[JPT][hapmap]
rs7718810	0.94[JPT][hapmap]
rs878073	0.94[JPT][hapmap]
rs878076	0.94[JPT][hapmap]
rs882253	0.94[JPT][hapmap]
rs888844	0.91[JPT][hapmap]
rs9326869	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs959949	0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs33553	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112311600-112314800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:112311600-112315200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:112311800-112314600	Active TSS	Fetal Intestine Large	intestine
4	chr5:112311800-112314800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr5:112311800-112315000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr5:112311800-112315200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:112312000-112314600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr5:112312000-112314600	Active TSS	NHDF-Ad	bronchial
9	chr5:112312000-112314800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr5:112312000-112314800	Active TSS	NHLF	lung
11	chr5:112312000-112315200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:112312000-112315200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr5:112312000-112315400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:112312000-112315600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:112312000-112316000	Active TSS	K562	blood
16	chr5:112312200-112314800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:112312200-112316600	Active TSS	GM12878-XiMat	blood
18	chr5:112312600-112315600	Active TSS	Right Atrium	heart
19	chr5:112313000-112314800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr5:112313000-112316400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:112313200-112314600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr5:112313200-112315400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:112313200-112315800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr5:112313200-112329000	Weak transcription	Spleen	Spleen
25	chr5:112313400-112314600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:112313400-112314600	Active TSS	Brain Germinal Matrix	brain
27	chr5:112313400-112314800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr5:112313600-112314600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr5:112313600-112316400	Enhancers	Fetal Brain Male	brain
30	chr5:112313800-112314600	Enhancers	Primary B cells from peripheral blood	blood
31	chr5:112313800-112314800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:112313800-112314800	Flanking Active TSS	Fetal Brain Female	brain
33	chr5:112313800-112315000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:112313800-112315000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:112313800-112315400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr5:112313800-112315600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:112313800-112315800	Flanking Active TSS	Dnd41	blood
38	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr5:112314000-112314800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr5:112314000-112314800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:112314000-112314800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr5:112314000-112314800	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr5:112314000-112314800	Enhancers	Brain Substantia Nigra	brain
44	chr5:112314000-112314800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr5:112314000-112315000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:112314000-112315600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr5:112314000-112315600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:112314000-112315800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr5:112314000-112315800	Flanking Active TSS	HUVEC	blood vessel
50	chr5:112314000-112316600	Weak transcription	Fetal Muscle Leg	muscle

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