Variant report

Variant	rs3118919
Chromosome Location	chr13:51160744-51160745
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1341637	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1638703	0.81[TSI][hapmap]
rs201762	0.87[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2225226	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2408045	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3116599	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3116600	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3116601	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3116602	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3116603	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3116604	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3116605	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3116606	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3116607	0.81[EUR][1000 genomes]
rs3116613	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3116615	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3116616	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116617	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118903	0.80[EUR][1000 genomes]
rs3118905	1.00[JPT][hapmap]
rs3118906	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3118909	0.84[EUR][1000 genomes]
rs3118910	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3118912	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3118913	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3118914	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3118915	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118920	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121212	1.00[ASW][hapmap]
rs7337757	0.86[AMR][1000 genomes];0.90[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
rs3118919	ATP7B	cis	parietal	SCAN
rs3118919	LPAR6	cis	parietal	SCAN

Chromatin state (count:35 , 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	chr13:51151000-51161800	Weak transcription	Right Atrium	heart
5	chr13:51151200-51169600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr13:51156200-51167600	Weak transcription	Fetal Kidney	kidney
7	chr13:51158400-51162200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:51158400-51164000	Enhancers	Fetal Muscle Leg	muscle
9	chr13:51159000-51161000	Enhancers	Left Ventricle	heart
10	chr13:51159200-51161000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:51159200-51161400	Enhancers	Fetal Stomach	stomach
12	chr13:51159200-51162000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr13:51159400-51161200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr13:51159400-51168000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr13:51159400-51168000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr13:51159400-51170600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr13:51159600-51161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr13:51159600-51161200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:51159600-51161400	Enhancers	Fetal Lung	lung
20	chr13:51159600-51165000	Enhancers	Fetal Heart	heart
21	chr13:51159600-51168400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:51159800-51161200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:51159800-51161400	Weak transcription	Osteobl	bone
24	chr13:51160000-51161000	Weak transcription	NHDF-Ad	bronchial
25	chr13:51160000-51161400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:51160000-51163600	Enhancers	Placenta	Placenta
27	chr13:51160000-51166600	Enhancers	Fetal Thymus	thymus
28	chr13:51160000-51168000	Weak transcription	Thymus	Thymus
29	chr13:51160200-51161200	Enhancers	Fetal Muscle Trunk	muscle
30	chr13:51160200-51162000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:51160200-51174000	Enhancers	Primary B cells from peripheral blood	blood
32	chr13:51160400-51161800	Weak transcription	Lung	lung
33	chr13:51160400-51162000	Weak transcription	Right Ventricle	heart
34	chr13:51160400-51163400	Weak transcription	Adipose Nuclei	Adipose
35	chr13:51160600-51164000	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links