Variant report

Variant	rs7126245
Chromosome Location	chr11:10615473-10615474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMPD3-1	chr11:10615367-10615527	ENSG00000177112.3

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10219205	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1062912	0.81[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10770126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840438	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10840440	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10840441	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs10840443	0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10840444	0.87[ASN][1000 genomes]
rs10840445	0.85[ASN][1000 genomes]
rs10840446	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10840448	0.82[ASN][1000 genomes]
rs11042876	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11042877	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042882	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042883	1.00[JPT][hapmap]
rs11042893	0.83[ASN][1000 genomes]
rs11042894	0.83[ASN][1000 genomes]
rs11042895	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11042897	0.82[ASN][1000 genomes]
rs11042898	0.84[ASN][1000 genomes]
rs11827503	0.84[ASN][1000 genomes]
rs12280275	0.86[ASN][1000 genomes]
rs12288969	0.81[ASN][1000 genomes]
rs12576545	0.84[ASN][1000 genomes]
rs12576547	0.82[ASN][1000 genomes]
rs16907989	0.81[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1964537	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2241489	0.83[ASN][1000 genomes]
rs2278125	0.80[CHB][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2288236	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34988160	0.82[ASN][1000 genomes]
rs3741033	0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3741034	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs3741042	0.86[ASN][1000 genomes]
rs4910162	0.82[ASN][1000 genomes]
rs7114453	0.84[ASN][1000 genomes]
rs7114603	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7115310	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7115735	0.82[ASN][1000 genomes]
rs7118551	0.81[ASN][1000 genomes]
rs724723	0.84[ASN][1000 genomes]
rs7358373	0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs746164	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs749045	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs881436	0.80[ASN][1000 genomes]
rs918981	0.85[ASN][1000 genomes]
rs964425	0.82[ASN][1000 genomes]
rs964426	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7126245	MRVI1	cis	multi-tissue	Pritchard
rs7126245	MRVI1	cis	normal skin	skin_eQTL
rs7126245	RNF141	cis	parietal	SCAN
rs7126245	AMPD3	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10586400-10620400	Weak transcription	Brain Anterior Caudate	brain
2	chr11:10592400-10622600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:10595000-10629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:10595000-10632800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:10597200-10625800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:10603600-10621800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr11:10605200-10620400	Weak transcription	Fetal Thymus	thymus
8	chr11:10605800-10622200	Weak transcription	Spleen	Spleen
9	chr11:10606000-10620400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:10607200-10616800	Enhancers	Placenta	Placenta
11	chr11:10607400-10626000	Weak transcription	Fetal Lung	lung
12	chr11:10608400-10616000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr11:10608800-10625400	Weak transcription	Adipose Nuclei	Adipose
14	chr11:10609600-10616000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:10609600-10619600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:10609600-10620800	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:10610200-10617000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:10610800-10618800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:10611000-10616000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:10611400-10615800	Weak transcription	K562	blood
21	chr11:10611600-10625000	Weak transcription	Brain Substantia Nigra	brain
22	chr11:10612000-10615600	Enhancers	NHEK	skin
23	chr11:10612400-10616800	Enhancers	HMEC	breast
24	chr11:10612600-10616200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:10612800-10617400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:10613200-10616000	Genic enhancers	Stomach Smooth Muscle	stomach
27	chr11:10613400-10619400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:10613400-10620600	Weak transcription	Lung	lung
29	chr11:10613600-10619400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr11:10613800-10615800	Weak transcription	Hela-S3	cervix
31	chr11:10613800-10620600	Weak transcription	Psoas Muscle	Psoas
32	chr11:10614000-10621200	Weak transcription	HSMMtube	muscle
33	chr11:10614400-10619400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:10614600-10616000	Enhancers	Esophagus	oesophagus
35	chr11:10614600-10616400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:10614800-10615800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:10614800-10616000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:10614800-10616000	Strong transcription	Fetal Intestine Large	intestine
39	chr11:10614800-10616000	Strong transcription	Fetal Intestine Small	intestine
40	chr11:10614800-10616000	Strong transcription	Ovary	ovary
41	chr11:10614800-10616200	Strong transcription	Fetal Stomach	stomach
42	chr11:10614800-10618400	Weak transcription	Primary B cells from cord blood	blood
43	chr11:10614800-10619200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:10614800-10620000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr11:10615000-10616200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:10615000-10617800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr11:10615000-10621000	Weak transcription	Fetal Kidney	kidney
48	chr11:10615000-10621200	Weak transcription	NHLF	lung
49	chr11:10615000-10625600	Weak transcription	Osteobl	bone
50	chr11:10615200-10615600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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