Variant report

Variant	rs12487863
Chromosome Location	chr3:47159252-47159253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47151756..47154654-chr3:47157875..47159694,2	K562	blood:
2	chr3:47157859..47160237-chr3:47204049..47206220,2	K562	blood:
3	chr3:47157453..47160237-chr3:47204049..47206459,2	K562	blood:

Variant related genes	Relation type
ENSG00000181555	Chromatin interaction
ENSG00000227398	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12486248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12489851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs12490244	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490251	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491419	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12492463	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12493723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495173	0.86[ASN][1000 genomes]
rs12495438	0.92[ASN][1000 genomes]
rs17079425	1.00[JPT][hapmap]
rs17079512	0.89[ASN][1000 genomes]
rs17079543	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2291721	0.89[AMR][1000 genomes]
rs3733093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs3816531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3821879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3933020	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4082156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4627772	0.89[ASN][1000 genomes]
rs4683318	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683323	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58206566	0.92[ASN][1000 genomes]
rs59601660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60285825	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61364027	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7372834	0.84[AMR][1000 genomes]
rs7638049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][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	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
5	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1002970	chr3:47120592-47170607	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47126400-47159800	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr3:47126800-47168200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:47139600-47161800	Weak transcription	Fetal Brain Female	brain
4	chr3:47139800-47163200	Weak transcription	A549	lung
5	chr3:47140000-47175600	Weak transcription	Small Intestine	intestine
6	chr3:47144200-47170800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:47145800-47175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:47146400-47164600	Weak transcription	Psoas Muscle	Psoas
9	chr3:47149600-47160000	Strong transcription	Liver	Liver
10	chr3:47149800-47159600	Strong transcription	Dnd41	blood
11	chr3:47150600-47160600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:47150800-47161000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:47150800-47161400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:47150800-47166600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:47151200-47164400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:47151200-47164400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:47151200-47167400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:47151400-47159600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:47151400-47161600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:47151600-47159800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:47151800-47160600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:47152000-47159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:47152000-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:47152200-47159800	Strong transcription	Fetal Intestine Large	intestine
25	chr3:47152400-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:47152400-47166000	Strong transcription	Placenta	Placenta
27	chr3:47154000-47164600	Weak transcription	Pancreas	Pancrea
28	chr3:47155000-47159600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:47155200-47164600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:47155200-47165400	Weak transcription	Fetal Brain Male	brain
31	chr3:47155200-47172600	Weak transcription	Colonic Mucosa	Colon
32	chr3:47155400-47161600	Weak transcription	Aorta	Aorta
33	chr3:47155400-47162200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:47155400-47164400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:47155400-47164600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:47155400-47164600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:47155400-47164600	Weak transcription	Gastric	stomach
38	chr3:47155400-47164600	Weak transcription	Ovary	ovary
39	chr3:47155400-47165400	Weak transcription	Spleen	Spleen
40	chr3:47155400-47183800	Weak transcription	Esophagus	oesophagus
41	chr3:47155600-47159600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:47155600-47161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:47155600-47161600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:47155600-47161600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:47155600-47162000	Weak transcription	Thymus	Thymus
46	chr3:47155600-47164200	Weak transcription	Lung	lung
47	chr3:47155600-47164400	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:47155800-47163400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:47155800-47163600	Weak transcription	Fetal Heart	heart
50	chr3:47155800-47164600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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