Variant report

Variant	rs2402749
Chromosome Location	chr7:124389723-124389724
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10085793	0.83[ASN][1000 genomes]
rs10085867	0.83[ASN][1000 genomes]
rs10085888	0.83[ASN][1000 genomes]
rs10156168	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10227821	0.84[ASN][1000 genomes]
rs10228376	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10228682	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10233306	0.80[ASN][1000 genomes]
rs10233589	0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs10236782	0.82[ASN][1000 genomes]
rs10243736	0.84[ASN][1000 genomes]
rs10250202	0.84[ASN][1000 genomes]
rs10250911	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10257255	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10260227	0.84[ASN][1000 genomes]
rs10260710	0.84[ASN][1000 genomes]
rs10261610	0.84[ASN][1000 genomes]
rs10263573	0.92[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10269011	0.81[ASN][1000 genomes]
rs10270784	0.84[ASN][1000 genomes]
rs10271687	0.80[ASN][1000 genomes]
rs10272583	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10954045	0.80[ASN][1000 genomes]
rs10954048	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs11975788	0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11978628	0.84[ASN][1000 genomes]
rs11978656	0.83[ASN][1000 genomes]
rs11979724	0.84[ASN][1000 genomes]
rs11980925	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs11983251	0.84[ASN][1000 genomes]
rs12154816	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12155120	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs12530981	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs12536575	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12538333	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12666427	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs12673697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13228116	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1468377	0.84[ASN][1000 genomes]
rs1468378	0.84[ASN][1000 genomes]
rs1481341	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1557969	0.95[ASN][1000 genomes]
rs16871295	0.84[ASN][1000 genomes]
rs17147494	0.83[ASN][1000 genomes]
rs17147496	0.84[ASN][1000 genomes]
rs17147583	0.82[ASN][1000 genomes]
rs1904975	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2040926	0.84[ASN][1000 genomes]
rs2079368	0.83[ASN][1000 genomes]
rs2107936	0.81[ASN][1000 genomes]
rs2219954	0.86[JPT][hapmap]
rs2267707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267708	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286173	0.84[ASN][1000 genomes]
rs2286174	0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2299902	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2299903	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301930	0.84[ASN][1000 genomes]
rs2402753	0.84[ASN][1000 genomes]
rs2402755	0.84[ASN][1000 genomes]
rs2896360	0.83[ASN][1000 genomes]
rs2896361	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3213667	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs33935352	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34014883	0.83[ASN][1000 genomes]
rs34204767	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34600520	0.80[ASN][1000 genomes]
rs35184624	0.84[ASN][1000 genomes]
rs35332300	0.84[ASN][1000 genomes]
rs3807544	0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs3815221	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4283967	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4311608	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs4377885	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4422720	0.80[ASN][1000 genomes]
rs4463363	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4552839	0.80[ASN][1000 genomes]
rs4584095	0.80[ASN][1000 genomes]
rs4728009	0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4728010	0.83[ASN][1000 genomes]
rs4728011	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4728012	0.83[ASN][1000 genomes]
rs4731207	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4731208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4731216	0.92[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4731217	0.83[ASN][1000 genomes]
rs4731218	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4731221	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4731222	0.83[ASN][1000 genomes]
rs4731223	0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4731224	0.80[ASN][1000 genomes]
rs57458159	0.80[ASN][1000 genomes]
rs62478914	0.84[ASN][1000 genomes]
rs6466948	0.84[ASN][1000 genomes]
rs6466949	0.84[ASN][1000 genomes]
rs6466950	0.84[ASN][1000 genomes]
rs6466952	0.80[ASN][1000 genomes]
rs6466955	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6945104	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6961292	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6963177	0.84[ASN][1000 genomes]
rs6968500	0.84[ASN][1000 genomes]
rs6973812	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs71576215	0.84[ASN][1000 genomes]
rs720615	0.84[ASN][1000 genomes]
rs720616	0.84[ASN][1000 genomes]
rs727506	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7357296	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7778544	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs7778956	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7781148	0.84[ASN][1000 genomes]
rs7783781	0.84[ASN][1000 genomes]
rs7789859	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7792883	0.84[ASN][1000 genomes]
rs7793258	0.84[ASN][1000 genomes]
rs7795492	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7796150	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7799938	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs7811607	0.84[ASN][1000 genomes]
rs7811608	0.84[ASN][1000 genomes]
rs886704	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs962863	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9886177	0.91[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv3446198	chr7:124358002-124586856	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2402749	RP11-3B12.1	cis	Artery Tibial	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124378600-124396600	Weak transcription	Fetal Lung	lung
2	chr7:124383000-124394800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:124385000-124394800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:124385200-124396600	Weak transcription	Aorta	Aorta
5	chr7:124385800-124395000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:124387000-124391400	Weak transcription	Fetal Brain Female	brain
7	chr7:124387000-124394800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:124387400-124392000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:124387400-124392000	Weak transcription	NHLF	lung
10	chr7:124387400-124395200	Weak transcription	Liver	Liver
11	chr7:124387400-124402600	Weak transcription	Fetal Stomach	stomach
12	chr7:124387600-124391200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:124387600-124392000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:124387600-124396600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:124387800-124401200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:124388400-124390400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:124388800-124390000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr7:124389000-124389800	Active TSS	Brain Cingulate Gyrus	brain
19	chr7:124389000-124391200	Active TSS	Brain Anterior Caudate	brain
20	chr7:124389400-124389800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:124389400-124389800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr7:124389400-124389800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr7:124389400-124391600	Active TSS	Brain Hippocampus Middle	brain
24	chr7:124389600-124391000	Active TSS	Brain Angular Gyrus	brain
25	chr7:124389600-124391000	Active TSS	Brain Substantia Nigra	brain
26	chr7:124389600-124392200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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