Variant report

Variant	rs1057474
Chromosome Location	chr5:112363954-112363955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112361859..112364300-chr5:112370845..112373439,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11749921	0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12517398	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13156493	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs13159449	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13177101	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs13186334	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13445	0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1363333	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17372511	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2112454	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2227948	0.83[ASN][1000 genomes]
rs2416300	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3185733	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33544	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs33551	0.86[JPT][hapmap]
rs33554	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs33557	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs33568	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs33569	0.80[CHB][hapmap]
rs3857434	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4073358	0.84[ASN][1000 genomes]
rs4073359	0.81[ASN][1000 genomes]
rs4074190	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4075350	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4301226	0.85[JPT][hapmap]
rs4428399	0.83[ASN][1000 genomes]
rs4705745	0.83[ASN][1000 genomes]
rs4705749	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705750	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705752	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705755	0.83[ASN][1000 genomes]
rs4705756	0.84[ASN][1000 genomes]
rs4705758	0.86[JPT][hapmap]
rs4778	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6594665	0.85[JPT][hapmap]
rs6869100	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6877769	0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6893389	0.81[JPT][hapmap]
rs6894219	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6894937	0.81[ASN][1000 genomes]
rs7670	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7701781	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7732198	0.81[JPT][hapmap]
rs9122	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9784647	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1057474	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs1057474	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs1057474	MCC	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
8	chr5:112334000-112365200	Strong transcription	Placenta	Placenta
9	chr5:112349800-112366600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:112352400-112367800	Strong transcription	Liver	Liver
11	chr5:112354600-112365400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:112356200-112365000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:112356200-112365000	Strong transcription	Adipose Nuclei	Adipose
14	chr5:112356400-112365400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:112357600-112364600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:112357800-112364400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:112358000-112364600	Strong transcription	NHDF-Ad	bronchial
18	chr5:112358200-112364200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:112358600-112365400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:112358800-112364200	Strong transcription	NHEK	skin
21	chr5:112358800-112365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:112358800-112366000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:112359200-112364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:112359600-112364600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:112359600-112365400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:112359600-112365800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:112359600-112367800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:112359800-112364000	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr5:112359800-112364000	Strong transcription	HUVEC	blood vessel
30	chr5:112359800-112364000	Strong transcription	K562	blood
31	chr5:112359800-112364800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:112359800-112365400	Strong transcription	Left Ventricle	heart
33	chr5:112359800-112365600	Strong transcription	Fetal Muscle Leg	muscle
34	chr5:112359800-112365800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr5:112360000-112365400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:112360000-112379000	Weak transcription	Small Intestine	intestine
37	chr5:112360200-112365400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:112360200-112368600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:112360400-112364000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:112360400-112364800	Strong transcription	HMEC	breast
41	chr5:112360400-112367200	Weak transcription	GM12878-XiMat	blood
42	chr5:112360400-112367600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:112360400-112368000	Weak transcription	Primary B cells from cord blood	blood
44	chr5:112360400-112368400	Weak transcription	Stomach Mucosa	stomach
45	chr5:112360600-112364200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:112360800-112364800	Strong transcription	Fetal Intestine Large	intestine
47	chr5:112361000-112364800	Strong transcription	Fetal Thymus	thymus
48	chr5:112361000-112368000	Strong transcription	Fetal Stomach	stomach
49	chr5:112361400-112364000	Strong transcription	Fetal Lung	lung
50	chr5:112361400-112364000	Strong transcription	Lung	lung

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