Variant report

Variant	rs6778589
Chromosome Location	chr3:99728691-99728692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12486901	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12487143	0.86[CEU][hapmap]
rs12489030	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12494994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496041	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1387649	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1871847	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs3921767	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4928233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4928236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928240	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414382	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792339	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6800456	0.88[JPT][hapmap]
rs73859922	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7431827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632345	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7634628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641782	0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs7652706	0.93[CEU][hapmap]
rs9824430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9827744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9872339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6778589	ZPLD1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99721400-99729400	Enhancers	HUVEC	blood vessel
4	chr3:99722400-99741400	Weak transcription	Aorta	Aorta
5	chr3:99722400-99751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:99722600-99741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:99724000-99729000	Enhancers	Fetal Kidney	kidney
8	chr3:99725000-99745600	Weak transcription	Left Ventricle	heart
9	chr3:99725200-99743600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:99726000-99729000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:99726000-99733800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:99726200-99728800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:99726200-99729600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:99726400-99748200	Weak transcription	HSMM	muscle
15	chr3:99727000-99729000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr3:99727000-99746400	Weak transcription	Right Atrium	heart
17	chr3:99727200-99728800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:99727200-99741200	Weak transcription	NHEK	skin
19	chr3:99727200-99741800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:99727400-99741000	Weak transcription	Psoas Muscle	Psoas
21	chr3:99727600-99733600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:99727600-99741800	Weak transcription	Fetal Intestine Small	intestine
23	chr3:99728000-99729200	Enhancers	Stomach Mucosa	stomach
24	chr3:99728000-99729400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:99728200-99728800	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr3:99728400-99728800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:99728400-99729200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:99728600-99728800	Enhancers	Fetal Lung	lung
30	chr3:99728600-99729000	Weak transcription	Fetal Heart	heart

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