Variant report

Variant	rs33554
Chromosome Location	chr5:112312736-112312737
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112225010..112227732-chr5:112311163..112313003,2	K562	blood:
2	chr5:112255209..112259355-chr5:112310614..112316433,9	K562	blood:
3	chr5:112253961..112259306-chr5:112310933..112315767,8	K562	blood:
4	chr5:89770106..89771750-chr5:112311690..112313641,2	K562	blood:
5	chr5:112255914..112262078-chr5:112308752..112315375,16	MCF-7	breast:
6	chr5:112195538..112198310-chr5:112312375..112313895,2	K562	blood:
7	chr22:29196449..29197081-chr5:112312184..112312841,2	HCT-116	colon:
8	chr5:112255746..112257849-chr5:112312359..112314246,3	MCF-7	breast:
9	chr5:112312686..112316155-chr5:112325860..112328052,3	K562	blood:
10	chr21:30396749..30397708-chr5:112312126..112312767,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000176055	Chromatin interaction
ENSG00000129625	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000273254	Chromatin interaction
ENSG00000272869	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000153037	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000212643	Chromatin interaction
ENSG00000156256	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1057474	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs13156493	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs13177101	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs13186334	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs13445	0.86[CHB][hapmap]
rs1363333	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1549181	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs17372511	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2112454	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2416300	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3185733	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs33544	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33545	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33548	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33549	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs33551	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33552	0.96[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs33557	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	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs33559	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33560	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33561	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs33566	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs33568	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33569	0.85[ASN][1000 genomes]
rs3857434	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4075350	0.90[JPT][hapmap]
rs4705749	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4705750	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4705752	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4778	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7670	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7701781	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs9122	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs9784647	0.81[CEU][hapmap];0.85[CHB][hapmap];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs33554	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs33554	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs33554	MCC	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112311600-112312800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112311600-112313800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:112311600-112313800	Active TSS	Colonic Mucosa	Colon
4	chr5:112311600-112314000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:112311600-112314200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr5:112311600-112314400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:112311600-112314800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:112311600-112315200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:112311800-112313200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:112311800-112313800	Active TSS	Esophagus	oesophagus
11	chr5:112311800-112314000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr5:112311800-112314000	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr5:112311800-112314000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:112311800-112314000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:112311800-112314000	Active TSS	Stomach Mucosa	stomach
16	chr5:112311800-112314200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr5:112311800-112314200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:112311800-112314200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:112311800-112314200	Active TSS	Fetal Muscle Trunk	muscle
20	chr5:112311800-112314200	Active TSS	Left Ventricle	heart
21	chr5:112311800-112314200	Active TSS	Ovary	ovary
22	chr5:112311800-112314200	Active TSS	Psoas Muscle	Psoas
23	chr5:112311800-112314200	Active TSS	Right Ventricle	heart
24	chr5:112311800-112314200	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr5:112311800-112314400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:112311800-112314600	Active TSS	Fetal Intestine Large	intestine
27	chr5:112311800-112314800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr5:112311800-112315000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr5:112311800-112315200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr5:112312000-112313200	Active TSS	Primary T cells from cord blood	blood
31	chr5:112312000-112313200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
32	chr5:112312000-112313200	Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr5:112312000-112313200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:112312000-112313200	Active TSS	Spleen	Spleen
35	chr5:112312000-112313400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:112312000-112313400	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr5:112312000-112313400	Active TSS	Monocytes-CD14+_RO01746	blood
38	chr5:112312000-112313600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:112312000-112313600	Active TSS	Brain Substantia Nigra	brain
40	chr5:112312000-112313600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr5:112312000-112313800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:112312000-112313800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:112312000-112313800	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr5:112312000-112313800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:112312000-112313800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr5:112312000-112313800	Active TSS	Brain Hippocampus Middle	brain
47	chr5:112312000-112313800	Active TSS	Fetal Heart	heart
48	chr5:112312000-112313800	Active TSS	Fetal Intestine Small	intestine
49	chr5:112312000-112313800	Active TSS	Gastric	stomach
50	chr5:112312000-112313800	Active TSS	Lung	lung

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