Variant report

Variant	rs3751380
Chromosome Location	chr13:49151419-49151420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RCBTB2-3	chr13:49151110-49151995	NONHSAT033722

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1547660	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1926595	0.97[ASN][1000 genomes]
rs1926596	0.88[ASN][1000 genomes]
rs1926597	0.97[ASN][1000 genomes]
rs198564	0.82[ASN][1000 genomes]
rs198568	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198571	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198574	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198575	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198576	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198577	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198606	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs198609	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198610	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2274400	0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs28414460	0.88[ASN][1000 genomes]
rs2854362	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs28646083	0.88[ASN][1000 genomes]
rs28674973	0.81[ASN][1000 genomes]
rs2897587	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3092898	0.85[ASN][1000 genomes]
rs398158	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs403390	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs406098	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4151601	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs425834	0.89[CHB][hapmap]
rs427686	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs61074776	0.97[ASN][1000 genomes]
rs6561448	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6561457	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6561461	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.97[ASN][1000 genomes]
rs7325962	0.87[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs7326934	0.84[YRI][hapmap]
rs7329039	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7329865	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs73486867	0.97[ASN][1000 genomes]
rs73495016	0.85[ASN][1000 genomes]
rs7985825	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7987935	0.88[ASN][1000 genomes]
rs7992129	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7995216	0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7996186	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7996402	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7998781	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8001241	0.87[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8002565	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9316385	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9316396	0.85[TSI][hapmap]
rs9316401	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9331959	0.88[ASN][1000 genomes]
rs9331965	0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9331973	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9332054	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs9591172	0.97[ASN][1000 genomes]
rs9591177	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9591178	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9595929	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS 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 target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49137200-49153000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr13:49143000-49153600	Weak transcription	Liver	Liver
4	chr13:49144800-49153000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr13:49145800-49152800	Weak transcription	Placenta	Placenta
6	chr13:49146000-49153200	Weak transcription	Stomach Mucosa	stomach
7	chr13:49146000-49153400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:49146000-49153800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr13:49146400-49154000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:49146800-49157400	Weak transcription	HSMMtube	muscle
11	chr13:49147400-49152800	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:49147600-49160800	Weak transcription	Thymus	Thymus
13	chr13:49148000-49153600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:49148400-49153200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr13:49148400-49153800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr13:49148400-49153800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr13:49148400-49158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr13:49148400-49159000	Weak transcription	Pancreas	Pancrea
19	chr13:49148400-49160600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr13:49148600-49153000	Weak transcription	Adipose Nuclei	Adipose
21	chr13:49148600-49153800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:49148800-49151600	Weak transcription	Spleen	Spleen
23	chr13:49148800-49152800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr13:49148800-49152800	Weak transcription	Fetal Muscle Leg	muscle
25	chr13:49148800-49152800	Weak transcription	Right Atrium	heart
26	chr13:49148800-49153600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr13:49148800-49153800	Weak transcription	Brain Substantia Nigra	brain
28	chr13:49148800-49157800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr13:49149400-49153200	Weak transcription	Left Ventricle	heart
30	chr13:49150000-49152800	Weak transcription	HepG2	liver
31	chr13:49150400-49152000	Enhancers	Dnd41	blood
32	chr13:49150400-49152600	Enhancers	GM12878-XiMat	blood
33	chr13:49150400-49154200	Enhancers	Fetal Thymus	thymus
34	chr13:49150600-49159400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr13:49150800-49151600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr13:49151000-49152600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr13:49151000-49153200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:49151200-49152600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr13:49151400-49151600	Enhancers	Lung	lung
40	chr13:49151400-49151600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr13:49151400-49152200	Enhancers	Esophagus	oesophagus

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