Variant report

Variant	rs1402152
Chromosome Location	chr3:46574418-46574419
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	chr3:46567191..46569704-chr3:46574346..46575998,2	K562	blood:
2	chr3:46568691..46571329-chr3:46573292..46576453,3	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10865942	0.90[YRI][hapmap]
rs11713015	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492797	0.94[AFR][1000 genomes]
rs1520493	0.86[ASN][1000 genomes]
rs17078944	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373255	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34667937	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6791703	0.94[LWK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs6801759	0.81[ASN][1000 genomes]
rs7621549	0.94[AFR][1000 genomes]
rs939421	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs9827559	0.80[AFR][1000 genomes]
rs9839075	0.91[AFR][1000 genomes]
rs9848284	0.94[AFR][1000 genomes]
rs9848648	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849400	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv876737	chr3:46569721-46595431	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1402152	TRAIP	cis	parietal	SCAN
rs1402152	TDGF1	cis	parietal	SCAN
rs1402152	CELSR3	cis	cerebellum	SCAN
rs1402152	KIF9	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46541000-46580200	Weak transcription	Fetal Heart	heart
2	chr3:46544800-46599400	Weak transcription	Right Atrium	heart
3	chr3:46549200-46585400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:46549400-46579000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:46549600-46578600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:46556400-46591000	Weak transcription	Psoas Muscle	Psoas
7	chr3:46557800-46578400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:46558400-46591000	Weak transcription	Gastric	stomach
9	chr3:46559000-46580000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:46559400-46578000	Weak transcription	HSMMtube	muscle
11	chr3:46559800-46580400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:46560200-46574600	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:46562400-46578800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:46562600-46578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:46566200-46577600	Weak transcription	Fetal Thymus	thymus
16	chr3:46567200-46586000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:46568000-46578600	Weak transcription	Spleen	Spleen
18	chr3:46568800-46578000	Weak transcription	Primary T cells from cord blood	blood
19	chr3:46569000-46577800	Weak transcription	Right Ventricle	heart
20	chr3:46569000-46578800	Weak transcription	Liver	Liver
21	chr3:46569000-46584200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:46569200-46578400	Weak transcription	NHDF-Ad	bronchial
23	chr3:46569600-46580200	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:46569800-46577400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:46571000-46583800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:46571600-46578400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:46571600-46587000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:46573000-46574800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:46573400-46577400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:46573400-46577400	Weak transcription	K562	blood
31	chr3:46573400-46577600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:46573400-46577800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:46573400-46577800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:46574000-46577400	Weak transcription	Ovary	ovary
35	chr3:46574200-46574600	Enhancers	Dnd41	blood
36	chr3:46574400-46575200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:46574400-46577400	Weak transcription	Left Ventricle	heart

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