Variant report

Variant	rs11130092
Chromosome Location	chr3:46539864-46539865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10865942	0.83[CEU][hapmap]
rs12486039	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs62247795	0.81[AFR][1000 genomes]
rs6772937	1.00[JPT][hapmap];0.94[YRI][hapmap]
rs7374675	1.00[JPT][hapmap]
rs7430431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311391	1.00[JPT][hapmap]
rs9810340	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs9845968	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	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
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11130092	C3orf39	cis	cerebellum	SCAN
rs11130092	LRRC2	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46531200-46541600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:46531400-46540200	Weak transcription	Left Ventricle	heart
3	chr3:46533000-46544200	Weak transcription	Psoas Muscle	Psoas
4	chr3:46537200-46540000	Enhancers	Dnd41	blood
5	chr3:46537200-46546200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:46537200-46547000	Enhancers	Fetal Thymus	thymus
7	chr3:46537200-46550200	Enhancers	K562	blood
8	chr3:46537400-46542000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:46538000-46542200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:46538200-46540000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:46538200-46541600	Weak transcription	HSMM	muscle
12	chr3:46538200-46542000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:46538200-46546800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:46538400-46541200	Enhancers	Right Ventricle	heart
15	chr3:46538400-46541800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:46538400-46543000	Flanking Active TSS	Liver	Liver
17	chr3:46538600-46540400	Enhancers	Fetal Intestine Large	intestine
18	chr3:46538600-46541600	Weak transcription	NH-A	brain
19	chr3:46538600-46542000	Weak transcription	NHDF-Ad	bronchial
20	chr3:46538600-46544600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:46538800-46540400	Weak transcription	Fetal Heart	heart
22	chr3:46538800-46541000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:46538800-46541600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:46538800-46541600	Weak transcription	Osteobl	bone
25	chr3:46538800-46542200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:46538800-46543800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:46538800-46544400	Weak transcription	Right Atrium	heart
28	chr3:46538800-46546600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:46538800-46546800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:46539000-46542600	Weak transcription	HUVEC	blood vessel
31	chr3:46539000-46547200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:46539200-46541200	Enhancers	Fetal Muscle Leg	muscle
33	chr3:46539200-46542000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:46539200-46547600	Weak transcription	Spleen	Spleen
35	chr3:46539400-46543000	Weak transcription	Adipose Nuclei	Adipose
36	chr3:46539600-46540000	Enhancers	HSMMtube	muscle
37	chr3:46539600-46540800	Weak transcription	Primary T cells from cord blood	blood
38	chr3:46539800-46545400	Enhancers	Skeletal Muscle Female	skeletal muscle

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