Variant report

Variant	rs9835042
Chromosome Location	chr3:119901774-119901775
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119810057..119817149-chr3:119894256..119903865,22	MCF-7	breast:
2	chr3:119814363..119814891-chr3:119901625..119902317,2	Hela-S3	cervix:
3	chr3:119809943..119817218-chr3:119893934..119905581,30	MCF-7	breast:
4	chr3:119866110..119866732-chr3:119901277..119902219,2	MCF-7	breast:
5	chr3:119856115..119856652-chr3:119901410..119902399,3	MCF-7	breast:
6	chr3:119856245..119857039-chr3:119901270..119902216,3	MCF-7	breast:
7	chr3:119610502..119611380-chr3:119901494..119902513,3	MCF-7	breast:
8	chr3:119539576..119540526-chr3:119901251..119902442,9	MCF-7	breast:
9	chr3:119878912..119881945-chr3:119899697..119902370,3	MCF-7	breast:
10	chr3:119539565..119540086-chr3:119901520..119902156,2	MCF-7	breast:
11	chr3:119527283..119529245-chr3:119900596..119902132,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

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

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

rs_ID	r²[population]
rs10049457	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804550	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10934518	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934519	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934526	0.80[GIH][hapmap]
rs11710115	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11719262	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs11721221	0.90[JPT][hapmap]
rs11926867	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12489527	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13087908	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs13317104	0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1388754	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs1873070	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2014142	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029609	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2319669	0.80[GIH][hapmap]
rs3732363	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264984	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6772067	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180068	0.88[CEU][hapmap]
rs902793	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9844508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861883	0.86[TSI][hapmap]
rs9877813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9878040	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
10	nsv1008362	chr3:119901774-119919670	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9835042	PDIA5	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119892400-119914200	Weak transcription	Fetal Brain Female	brain
2	chr3:119896400-119921400	Weak transcription	Ovary	ovary
3	chr3:119897000-119902000	Weak transcription	NHLF	lung
4	chr3:119897000-119906000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:119897000-119913200	Weak transcription	Fetal Stomach	stomach
6	chr3:119897000-119921400	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:119897200-119901800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:119897200-119914800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:119897400-119908000	Weak transcription	Placenta	Placenta
10	chr3:119899000-119902200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:119899200-119902400	Enhancers	NHEK	skin
12	chr3:119899600-119902400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:119899600-119902400	Enhancers	HMEC	breast
14	chr3:119900200-119901800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:119900800-119915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:119901400-119901800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:119901400-119902400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:119901400-119902600	Enhancers	A549	lung
19	chr3:119901600-119902000	Enhancers	NH-A	brain
20	chr3:119901600-119902200	Enhancers	HSMMtube	muscle
21	chr3:119901600-119902400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:119901600-119902400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:119901600-119902400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:119901600-119902400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:119901600-119902400	Enhancers	HUVEC	blood vessel
26	chr3:119901600-119902400	Enhancers	NHDF-Ad	bronchial
27	chr3:119901600-119902400	Enhancers	Osteobl	bone
28	chr3:119901600-119902600	Enhancers	Hela-S3	cervix
29	chr3:119901600-119902600	Enhancers	HSMM	muscle
30	chr3:119901600-119902800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:119901600-119902800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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