Variant report

Variant	rs2289302
Chromosome Location	chr12:30843377-30843378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:30840558..30845484-chr12:30846630..30850252,8	K562	blood:
2	chr12:30840570..30842757-chr12:30843253..30846337,3	K562	blood:
3	chr12:30835899..30838387-chr12:30843101..30844801,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133704	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10444423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734793	0.85[ASN][1000 genomes]
rs10743729	1.00[ASW][hapmap];0.94[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];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771745	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771756	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771757	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771760	0.86[ASN][1000 genomes]
rs10771761	0.86[ASN][1000 genomes]
rs10771762	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771768	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843813	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843814	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843815	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843816	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843817	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843818	0.86[ASN][1000 genomes]
rs10843819	0.86[ASN][1000 genomes]
rs10843820	0.86[ASN][1000 genomes]
rs10843821	0.86[ASN][1000 genomes]
rs10843822	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843823	0.86[ASN][1000 genomes]
rs10843824	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843827	0.85[ASN][1000 genomes]
rs10843828	0.85[ASN][1000 genomes]
rs10843829	0.83[ASN][1000 genomes]
rs10843831	0.84[ASN][1000 genomes]
rs10843832	0.85[ASN][1000 genomes]
rs10843833	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10843834	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843835	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11051005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051008	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051010	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11051027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051045	0.86[ASN][1000 genomes]
rs11051047	0.85[ASN][1000 genomes]
rs11051048	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051049	0.85[ASN][1000 genomes]
rs11051050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051053	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11051061	0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11051063	0.81[ASN][1000 genomes]
rs11835180	0.85[ASN][1000 genomes]
rs12146709	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12303852	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12368923	0.86[ASN][1000 genomes]
rs12369125	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12370947	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12579616	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12809335	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12825440	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12826615	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830910	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241828	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278558	0.94[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2304630	0.90[JPT][hapmap]
rs35133495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35336533	0.86[ASN][1000 genomes]
rs36074842	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4082413	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4335626	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59177896	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61923728	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487928	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487934	0.86[ASN][1000 genomes]
rs6487936	0.86[ASN][1000 genomes]
rs6487939	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7299800	0.86[ASN][1000 genomes]
rs7304221	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7952744	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7955804	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957141	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7958274	0.83[ASN][1000 genomes]
rs7958276	0.85[ASN][1000 genomes]
rs7966063	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971762	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7971870	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7978343	0.93[CEU][hapmap]
rs7979718	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2289302	IPO8	cis	parietal	SCAN
rs2289302	IPO8	Cis_1M	lymphoblastoid	RTeQTL
rs2289302	IPO8	cis	cerebellum	SCAN
rs2289302	IPO8	cis	multi-tissue	Pritchard
rs2289302	IPO8	cis	Artery Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30767000-30844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:30780800-30847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:30785000-30847800	Weak transcription	Gastric	stomach
4	chr12:30785200-30846400	Weak transcription	Spleen	Spleen
5	chr12:30785400-30847200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:30810800-30843800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:30811000-30844200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:30812600-30844200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:30813200-30844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:30813600-30844200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:30815400-30845800	Weak transcription	Fetal Brain Male	brain
12	chr12:30816200-30844000	Weak transcription	NHEK	skin
13	chr12:30816400-30844200	Weak transcription	NHLF	lung
14	chr12:30821600-30844200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:30821800-30847200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:30821800-30847400	Weak transcription	Lung	lung
17	chr12:30822000-30846600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:30822600-30843800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:30822600-30845600	Weak transcription	Right Ventricle	heart
20	chr12:30822600-30846400	Weak transcription	Esophagus	oesophagus
21	chr12:30822600-30847400	Weak transcription	Aorta	Aorta
22	chr12:30822800-30844200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:30826000-30845600	Weak transcription	Brain Germinal Matrix	brain
24	chr12:30827000-30847000	Weak transcription	Colonic Mucosa	Colon
25	chr12:30827800-30844200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:30828200-30844200	Weak transcription	K562	blood
27	chr12:30829200-30844200	Weak transcription	Pancreas	Pancrea
28	chr12:30829600-30844200	Weak transcription	Small Intestine	intestine
29	chr12:30830400-30844000	Weak transcription	HMEC	breast
30	chr12:30830400-30844200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:30830400-30846600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:30831800-30844200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:30831800-30845600	Weak transcription	Brain Substantia Nigra	brain
34	chr12:30831800-30845600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:30831800-30846400	Weak transcription	Thymus	Thymus
36	chr12:30831800-30846600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:30831800-30846800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:30832000-30844200	Weak transcription	Left Ventricle	heart
39	chr12:30832000-30844200	Weak transcription	Ovary	ovary
40	chr12:30832200-30844200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:30832200-30846800	Weak transcription	Fetal Stomach	stomach
42	chr12:30832400-30845200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr12:30832600-30844200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:30832600-30845600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:30833000-30845400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:30833200-30844200	Weak transcription	Adipose Nuclei	Adipose
47	chr12:30833200-30845400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:30833400-30845600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:30833400-30845600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:30833600-30846600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links