Variant report

Variant	rs13156493
Chromosome Location	chr5:112334187-112334188
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112325917..112328748-chr5:112331994..112335756,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1057474	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11749921	0.81[JPT][hapmap]
rs12517398	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12654474	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13159449	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13171553	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13171773	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13176362	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13177101	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13183347	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13186334	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13445	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1363333	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1549181	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1549182	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17312754	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17372511	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2112454	0.84[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2416300	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3185733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs33544	0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs33545	0.88[ASN][1000 genomes]
rs33548	0.88[ASN][1000 genomes]
rs33551	0.88[JPT][hapmap]
rs33552	0.84[JPT][hapmap]
rs33554	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs33557	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs33568	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs33569	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs3857434	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4074190	0.83[JPT][hapmap]
rs4075350	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs4301226	0.82[JPT][hapmap]
rs4334876	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4705529	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705744	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705745	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4705749	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4705752	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4705758	0.83[JPT][hapmap]
rs4778	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes]
rs6594665	0.82[JPT][hapmap]
rs6869100	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6877769	0.82[JPT][hapmap]
rs6894219	0.82[JPT][hapmap]
rs7670	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7701781	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9122	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs9784647	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][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	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
rs13156493	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs13156493	DCP2	cis	Nerve Tibial	GTEx
rs13156493	DCP2	cis	multi-tissue	Pritchard
rs13156493	MCC	cis	Whole Blood	GTEx
rs13156493	DCP2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:112314000-112335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:112314000-112337200	Weak transcription	Lung	lung
4	chr5:112314000-112338200	Weak transcription	Gastric	stomach
5	chr5:112314200-112337000	Weak transcription	HSMMtube	muscle
6	chr5:112314200-112338200	Weak transcription	Aorta	Aorta
7	chr5:112314200-112341000	Weak transcription	Small Intestine	intestine
8	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
10	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
11	chr5:112314400-112338400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:112314800-112337200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
14	chr5:112315600-112339400	Weak transcription	Hela-S3	cervix
15	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
16	chr5:112315800-112334600	Weak transcription	Brain Germinal Matrix	brain
17	chr5:112316000-112337000	Weak transcription	A549	lung
18	chr5:112317000-112338200	Weak transcription	Left Ventricle	heart
19	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:112318000-112336400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:112319000-112335800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:112319400-112336800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:112319800-112363800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:112320200-112338200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:112320200-112338200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:112320400-112335800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:112320600-112337200	Weak transcription	Pancreas	Pancrea
30	chr5:112320600-112362600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:112321400-112363800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr5:112321600-112353800	Weak transcription	Fetal Heart	heart
34	chr5:112322200-112341000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr5:112322600-112362400	Weak transcription	Psoas Muscle	Psoas
36	chr5:112322800-112362400	Weak transcription	Esophagus	oesophagus
37	chr5:112324800-112336600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:112326000-112336800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr5:112326800-112337000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:112327400-112335200	Strong transcription	Fetal Thymus	thymus
42	chr5:112327400-112340600	Strong transcription	Primary B cells from cord blood	blood
43	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:112328000-112334600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:112328800-112341800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:112329400-112356800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr5:112330000-112335800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr5:112330200-112334800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr5:112330200-112335000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:112330200-112335200	Weak transcription	Fetal Intestine Small	intestine

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