Variant report

Variant	rs3116615
Chromosome Location	chr13:51158752-51158753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1327646	0.81[EUR][1000 genomes]
rs1341637	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1638703	0.81[TSI][hapmap]
rs201762	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2225226	0.93[EUR][1000 genomes]
rs2408045	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095527	0.81[EUR][1000 genomes]
rs3116598	0.80[EUR][1000 genomes]
rs3116599	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs3116600	0.86[EUR][1000 genomes]
rs3116601	0.86[EUR][1000 genomes]
rs3116602	0.92[EUR][1000 genomes]
rs3116603	0.92[EUR][1000 genomes]
rs3116604	0.92[EUR][1000 genomes]
rs3116605	0.92[EUR][1000 genomes]
rs3116606	0.92[EUR][1000 genomes]
rs3116607	0.83[EUR][1000 genomes]
rs3116613	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116616	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3116617	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3118903	0.82[EUR][1000 genomes]
rs3118905	1.00[JPT][hapmap]
rs3118906	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3118909	0.86[EUR][1000 genomes]
rs3118910	0.87[EUR][1000 genomes]
rs3118912	0.92[EUR][1000 genomes]
rs3118913	0.91[EUR][1000 genomes]
rs3118914	0.92[EUR][1000 genomes]
rs3118915	0.94[EUR][1000 genomes]
rs3118918	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3118919	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3118920	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7337757	0.92[EUR][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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3116615	LPAR6	cis	parietal	SCAN
rs3116615	ATP7B	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51147800-51160800	Weak transcription	Dnd41	blood
2	chr13:51149600-51162200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:51150400-51167400	Weak transcription	HepG2	liver
4	chr13:51150800-51160200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr13:51151000-51161800	Weak transcription	Right Atrium	heart
6	chr13:51151200-51159000	Weak transcription	Left Ventricle	heart
7	chr13:51151200-51169600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr13:51155400-51158800	Weak transcription	NHDF-Ad	bronchial
9	chr13:51155400-51159000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:51155800-51159200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:51156000-51160000	Weak transcription	Right Ventricle	heart
12	chr13:51156200-51159000	Weak transcription	Osteobl	bone
13	chr13:51156200-51159200	Weak transcription	Fetal Stomach	stomach
14	chr13:51156200-51160000	Weak transcription	Fetal Thymus	thymus
15	chr13:51156200-51167600	Weak transcription	Fetal Kidney	kidney
16	chr13:51156400-51158800	Weak transcription	HSMMtube	muscle
17	chr13:51156400-51159000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:51156400-51159000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:51157200-51159600	Weak transcription	Fetal Heart	heart
20	chr13:51158400-51162200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:51158400-51164000	Enhancers	Fetal Muscle Leg	muscle
22	chr13:51158600-51159400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr13:51158600-51159600	Enhancers	HUES6 Cell Line	embryonic stem cell

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