Variant report

Variant	rs1879328
Chromosome Location	chr3:46568157-46568158
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	chr3:46567191..46569704-chr3:46574346..46575998,2	K562	blood:
2	chr3:46564865..46566399-chr3:46567048..46569066,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs12492797	0.88[ASN][1000 genomes]
rs17078863	1.00[CEU][hapmap];0.82[LWK][hapmap]
rs17078878	1.00[CEU][hapmap]
rs1814973	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2269436	0.82[LWK][hapmap]
rs2888531	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34334514	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34478154	0.88[ASN][1000 genomes]
rs34504121	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35714147	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4521278	1.00[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs4683235	1.00[CEU][hapmap];0.82[LWK][hapmap]
rs4683241	1.00[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683242	1.00[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4683243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55786118	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55990714	0.89[ASN][1000 genomes]
rs59244195	0.87[EUR][1000 genomes]
rs59264692	0.88[ASN][1000 genomes]
rs60983021	0.87[EUR][1000 genomes]
rs6442000	0.91[EUR][1000 genomes]
rs67227548	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6774189	0.82[ASW][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6776621	1.00[CEU][hapmap]
rs67814017	0.86[ASN][1000 genomes]
rs6791703	0.86[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6791941	0.87[EUR][1000 genomes]
rs68018913	0.86[ASN][1000 genomes]
rs72900270	0.80[EUR][1000 genomes]
rs72900281	0.87[EUR][1000 genomes]
rs7428292	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743658	0.82[LWK][hapmap]
rs7621549	0.89[ASN][1000 genomes]
rs7629657	1.00[CEU][hapmap];0.82[LWK][hapmap]
rs7632776	0.89[ASN][1000 genomes]
rs7643332	0.87[EUR][1000 genomes]
rs867619	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs883738	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs883740	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9827559	0.89[ASN][1000 genomes]
rs9839075	0.89[ASN][1000 genomes]
rs9848284	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1879328	P4HA2	trans	brain	seeQTL
rs1879328	HSPA1B	trans	brain	seeQTL
rs1879328	HSPA1A	trans	brain	seeQTL
rs1879328	DNAJB4	trans	brain	seeQTL
rs1879328	HSPA4L	trans	brain	seeQTL

Chromatin state (count:36 , 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	chr3:46558000-46571400	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:46558400-46591000	Weak transcription	Gastric	stomach
10	chr3:46559000-46580000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:46559400-46578000	Weak transcription	HSMMtube	muscle
12	chr3:46559600-46573000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:46559800-46580400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:46560200-46574600	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:46560800-46569000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:46561800-46568200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:46562400-46578800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:46562600-46570200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:46562600-46572600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:46562600-46578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:46562800-46568400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:46562800-46568400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:46566200-46577600	Weak transcription	Fetal Thymus	thymus
24	chr3:46567200-46586000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:46567400-46568200	Weak transcription	Fetal Stomach	stomach
26	chr3:46567600-46568400	Enhancers	K562	blood
27	chr3:46567800-46569000	Strong transcription	Liver	Liver
28	chr3:46567800-46569600	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:46567800-46569800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr3:46567800-46574000	Strong transcription	Ovary	ovary
31	chr3:46567800-46574400	Strong transcription	Left Ventricle	heart
32	chr3:46568000-46568800	Strong transcription	Primary T cells from cord blood	blood
33	chr3:46568000-46569000	Strong transcription	Right Ventricle	heart
34	chr3:46568000-46569200	Strong transcription	NHDF-Ad	bronchial
35	chr3:46568000-46571000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:46568000-46578600	Weak transcription	Spleen	Spleen

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