Variant report

Variant	rs12654474
Chromosome Location	chr5:112334976-112334977
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	chr5:112325917..112328748-chr5:112331994..112335756,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12517398	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13156493	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13159449	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13171553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13171773	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13176362	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13177101	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13183347	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13186334	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13445	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1363333	0.83[AFR][1000 genomes]
rs1549182	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17312754	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17372511	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2112454	0.87[ASN][1000 genomes]
rs3185733	0.86[EUR][1000 genomes]
rs33544	0.86[ASN][1000 genomes]
rs33545	0.86[ASN][1000 genomes]
rs33548	0.86[ASN][1000 genomes]
rs3857434	0.82[EUR][1000 genomes]
rs4075350	0.80[EUR][1000 genomes]
rs4334876	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705529	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705531	0.81[AMR][1000 genomes]
rs4705744	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705745	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4705749	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705752	0.82[EUR][1000 genomes]
rs4778	0.90[EUR][1000 genomes]
rs6869100	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7670	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7701781	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9122	0.83[EUR][1000 genomes]
rs9784647	0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12654474	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs12654474	MCC	cis	Whole Blood	GTEx
rs12654474	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr5:112316000-112337000	Weak transcription	A549	lung
17	chr5:112317000-112338200	Weak transcription	Left Ventricle	heart
18	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:112318000-112336400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:112319000-112335800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:112319400-112336800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:112319800-112363800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:112320200-112338200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:112320200-112338200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:112320400-112335800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:112320600-112337200	Weak transcription	Pancreas	Pancrea
29	chr5:112320600-112362600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:112321400-112363800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:112321600-112353800	Weak transcription	Fetal Heart	heart
33	chr5:112322200-112341000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:112322600-112362400	Weak transcription	Psoas Muscle	Psoas
35	chr5:112322800-112362400	Weak transcription	Esophagus	oesophagus
36	chr5:112324800-112336600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:112326000-112336800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:112326800-112337000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:112327400-112335200	Strong transcription	Fetal Thymus	thymus
41	chr5:112327400-112340600	Strong transcription	Primary B cells from cord blood	blood
42	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:112328800-112341800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:112329400-112356800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr5:112330000-112335800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr5:112330200-112335000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:112330200-112335200	Weak transcription	Fetal Intestine Small	intestine
48	chr5:112330200-112335800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:112330200-112337000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr5:112330200-112338200	Weak transcription	Spleen	Spleen

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