Variant report

Variant	rs1530733
Chromosome Location	chr3:54389115-54389116
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	chr3:54375027..54375647-chr3:54388254..54389644,4	MCF-7	breast:
2	chr3:54375027..54375990-chr3:54387842..54389644,8	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12493552	1.00[ASW][hapmap]
rs12632768	0.83[CHD][hapmap]
rs13327362	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs1449330	0.87[CHD][hapmap]
rs1530732	1.00[ASW][hapmap];0.81[JPT][hapmap]
rs1868500	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs1992963	0.87[CHD][hapmap]
rs4974360	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs4974361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4974367	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4974370	0.87[CHD][hapmap]
rs6445664	0.81[JPT][hapmap]
rs73089434	0.92[ASN][1000 genomes]
rs73089448	0.92[ASN][1000 genomes]
rs73089451	0.92[ASN][1000 genomes]
rs7431094	0.89[ASN][1000 genomes]
rs7624727	0.81[JPT][hapmap]
rs9311528	0.93[CEU][hapmap];0.86[AMR][1000 genomes]
rs9311529	0.93[CEU][hapmap]
rs9835062	0.80[EUR][1000 genomes]
rs9841318	0.81[CEU][hapmap]
rs9851130	0.87[CHD][hapmap]
rs9862712	0.87[CHD][hapmap]
rs9862718	0.87[CHD][hapmap]
rs9870407	0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1530733	C3orf18	cis	parietal	SCAN
rs1530733	LCK	trans	lymphoblastoid	seeQTL
rs1530733	RBM15B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54380000-54391200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:54383400-54392600	Weak transcription	Right Ventricle	heart
3	chr3:54384000-54392400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:54387200-54392000	Enhancers	Fetal Lung	lung
5	chr3:54387200-54392600	Enhancers	Ovary	ovary
6	chr3:54387200-54394800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:54387400-54389400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:54387400-54390200	Enhancers	Left Ventricle	heart
9	chr3:54387400-54391800	Enhancers	Fetal Brain Male	brain
10	chr3:54387400-54392000	Enhancers	Adipose Nuclei	Adipose
11	chr3:54387600-54389200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr3:54387600-54389600	Enhancers	Colon Smooth Muscle	Colon
13	chr3:54387600-54394800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:54387600-54394800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:54387600-54396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:54387800-54393800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:54388000-54389200	Enhancers	Rectal Smooth Muscle	rectum
18	chr3:54388000-54389200	Weak transcription	Right Atrium	heart
19	chr3:54388000-54390200	Weak transcription	Fetal Brain Female	brain
20	chr3:54388200-54391800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:54388600-54389600	Enhancers	Fetal Muscle Leg	muscle
22	chr3:54388600-54389800	Weak transcription	Brain Anterior Caudate	brain
23	chr3:54388800-54389400	Enhancers	Brain Cingulate Gyrus	brain
24	chr3:54388800-54389600	Enhancers	Aorta	Aorta
25	chr3:54388800-54389800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:54388800-54389800	Weak transcription	Fetal Stomach	stomach
27	chr3:54388800-54391200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:54388800-54395400	Enhancers	Hela-S3	cervix
29	chr3:54389000-54389400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:54389000-54391200	Enhancers	Psoas Muscle	Psoas

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