Variant report

Variant	rs13159449
Chromosome Location	chr5:112345943-112345944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1057474	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12517398	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12654474	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13156493	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13171553	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13177101	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13186334	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13445	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1363333	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1549181	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1549182	0.81[ASN][1000 genomes]
rs17312754	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17372511	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2227948	0.80[EUR][1000 genomes]
rs3185733	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3857434	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4073358	0.80[EUR][1000 genomes]
rs4075350	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4334876	0.81[EUR][1000 genomes]
rs4705529	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705744	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705745	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705749	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705750	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705752	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705755	0.80[EUR][1000 genomes]
rs4778	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6869100	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7670	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7701781	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9122	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9784647	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13159449	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs13159449	DCP2	cis	Nerve Tibial	GTEx
rs13159449	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs13159449	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	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
3	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
4	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
5	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
6	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:112319800-112363800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:112320600-112362600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:112321400-112363800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:112321600-112353800	Weak transcription	Fetal Heart	heart
14	chr5:112322600-112362400	Weak transcription	Psoas Muscle	Psoas
15	chr5:112322800-112362400	Weak transcription	Esophagus	oesophagus
16	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:112329400-112356800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:112330200-112362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:112332400-112348600	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:112332400-112352400	Strong transcription	Dnd41	blood
22	chr5:112332400-112355800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
24	chr5:112332600-112349000	Weak transcription	Fetal Brain Female	brain
25	chr5:112332800-112352200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:112333000-112349400	Weak transcription	NHLF	lung
27	chr5:112333000-112359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:112333200-112362400	Weak transcription	Right Ventricle	heart
29	chr5:112334000-112365200	Strong transcription	Placenta	Placenta
30	chr5:112334200-112350400	Strong transcription	Fetal Intestine Large	intestine
31	chr5:112334200-112350400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr5:112334200-112352600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:112334800-112347600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr5:112334800-112352200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:112335000-112346400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:112335600-112350200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr5:112335600-112353200	Strong transcription	Fetal Thymus	thymus
38	chr5:112335800-112350600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr5:112335800-112351000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:112336400-112350200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:112336400-112350800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:112338600-112360800	Weak transcription	Aorta	Aorta
43	chr5:112339000-112349000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:112339200-112347800	Weak transcription	Left Ventricle	heart
45	chr5:112339200-112348400	Weak transcription	Brain Anterior Caudate	brain
46	chr5:112339200-112349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:112339200-112362400	Weak transcription	Pancreas	Pancrea
48	chr5:112339400-112348400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr5:112339400-112356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:112339400-112362000	Weak transcription	Gastric	stomach

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