Variant report

Variant	rs13445
Chromosome Location	chr5:112355908-112355909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112328300..112329801-chr5:112353472..112355961,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1057474	0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12517398	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12654474	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13156493	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13159449	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13171553	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13171773	0.83[EUR][1000 genomes]
rs13176362	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13177101	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13183347	0.85[EUR][1000 genomes]
rs13186334	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1363333	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1549181	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549182	0.80[EUR][1000 genomes]
rs17312754	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17372511	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2112454	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs2416300	0.95[CHB][hapmap]
rs3185733	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33544	0.85[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap]
rs33551	0.86[GIH][hapmap]
rs33554	0.86[CHB][hapmap]
rs33557	0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap]
rs33568	0.82[CHB][hapmap]
rs33569	0.81[CHD][hapmap];0.82[TSI][hapmap]
rs3857434	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4075350	0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4334876	0.86[EUR][1000 genomes]
rs4705529	0.81[EUR][1000 genomes]
rs4705744	0.82[EUR][1000 genomes]
rs4705745	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4705749	0.84[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705750	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705752	0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4778	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869100	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877769	0.81[CHD][hapmap]
rs6894219	0.83[CHD][hapmap]
rs7670	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7701781	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9122	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9784647	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]

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	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
4	nsv964924	chr5:112353388-112356719	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13445	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs13445	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs13445	DCP2	cis	multi-tissue	Pritchard
rs13445	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	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
2	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
3	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
4	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:112319800-112363800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:112320600-112362600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:112321400-112363800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:112322600-112362400	Weak transcription	Psoas Muscle	Psoas
12	chr5:112322800-112362400	Weak transcription	Esophagus	oesophagus
13	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:112329400-112356800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr5:112330200-112362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
18	chr5:112333000-112359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:112333200-112362400	Weak transcription	Right Ventricle	heart
20	chr5:112334000-112365200	Strong transcription	Placenta	Placenta
21	chr5:112338600-112360800	Weak transcription	Aorta	Aorta
22	chr5:112339200-112362400	Weak transcription	Pancreas	Pancrea
23	chr5:112339400-112356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:112339400-112362000	Weak transcription	Gastric	stomach
25	chr5:112340400-112362400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:112340400-112362600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:112340400-112362600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:112341600-112357600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:112342200-112362600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:112343200-112357000	Strong transcription	Primary B cells from cord blood	blood
31	chr5:112343200-112357000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:112345200-112356200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:112345400-112356000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:112349800-112359600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:112349800-112362400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:112349800-112366600	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:112350000-112360600	Weak transcription	Fetal Intestine Small	intestine
38	chr5:112350200-112356000	Weak transcription	NHLF	lung
39	chr5:112350200-112356000	Weak transcription	Osteobl	bone
40	chr5:112350200-112358000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:112350200-112361400	Weak transcription	Brain Substantia Nigra	brain
42	chr5:112350200-112361400	Weak transcription	Lung	lung
43	chr5:112350200-112361400	Weak transcription	Ovary	ovary
44	chr5:112350200-112362000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr5:112350200-112362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:112350200-112362600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr5:112350200-112362600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:112350200-112362600	Weak transcription	Brain Anterior Caudate	brain
49	chr5:112350200-112362800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:112350400-112356000	Weak transcription	HSMMtube	muscle

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