Variant report

Variant	rs3213989
Chromosome Location	chr12:42863801-42863802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42856522..42859149-chr12:42861270..42865700,4	K562	blood:
2	chr12:42858889..42861856-chr12:42862365..42864970,2	MCF-7	breast:
3	chr12:42763652..42765251-chr12:42861680..42863828,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1043652	0.92[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1043656	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880279	0.88[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs10880284	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs11181421	0.82[EUR][1000 genomes]
rs11181427	0.87[EUR][1000 genomes]
rs11181453	0.87[EUR][1000 genomes]
rs11181461	0.87[JPT][hapmap];0.91[MEX][hapmap]
rs11181484	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12229224	0.85[EUR][1000 genomes]
rs12229266	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230583	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12231335	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422938	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12423383	0.96[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs12425945	0.96[CEU][hapmap]
rs12578312	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1376931	0.96[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1629725	0.88[EUR][1000 genomes]
rs1669884	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1669888	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1669890	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1669891	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1669894	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669895	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669897	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669898	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669899	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1669900	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669901	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669903	0.96[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669905	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669911	0.87[EUR][1000 genomes]
rs1669912	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669913	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669914	0.88[EUR][1000 genomes]
rs1669935	0.88[EUR][1000 genomes]
rs1669937	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796354	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1796355	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796356	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796357	0.96[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796359	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796360	0.88[EUR][1000 genomes]
rs1796365	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796373	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796374	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796377	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796379	0.88[EUR][1000 genomes]
rs1796385	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796387	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1796389	0.96[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796392	0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1796395	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1796396	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1796397	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1796398	0.96[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2053946	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243465	0.96[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2406872	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406969	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2600911	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2600912	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2600916	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2600918	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2708063	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2708069	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2708075	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2708077	0.83[EUR][1000 genomes]
rs2708506	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2952653	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3747563	0.94[EUR][1000 genomes]
rs3761677	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs3827524	0.96[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs4603368	0.86[EUR][1000 genomes]
rs4768397	0.92[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs4768398	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs4768401	0.96[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs4768412	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134895	0.95[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs721447	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73122408	0.88[EUR][1000 genomes]
rs73122414	0.87[EUR][1000 genomes]
rs73122418	0.88[EUR][1000 genomes]
rs752767	0.88[EUR][1000 genomes]
rs896555	0.96[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs896556	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]

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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3213989	KIF21A	cis	cerebellum	SCAN
rs3213989	CPNE8	cis	parietal	SCAN
rs3213989	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
2	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
3	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
4	chr12:42849400-42864800	Strong transcription	Fetal Stomach	stomach
5	chr12:42850000-42866400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:42850200-42865000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:42850200-42865000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr12:42850200-42865800	Strong transcription	Osteobl	bone
9	chr12:42853400-42869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:42854000-42865800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:42854000-42868600	Weak transcription	Right Ventricle	heart
12	chr12:42854200-42865200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:42854200-42867400	Weak transcription	NHLF	lung
14	chr12:42854400-42864800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:42854400-42865200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr12:42854600-42864800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr12:42855200-42864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:42855400-42864000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:42855400-42865200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:42856200-42865800	Strong transcription	HMEC	breast
21	chr12:42856400-42864200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:42856800-42864000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:42859200-42864800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:42859200-42865200	Weak transcription	Fetal Intestine Small	intestine
25	chr12:42860200-42866800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:42860200-42868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:42860200-42870400	Weak transcription	Pancreas	Pancrea
28	chr12:42860200-42876200	Weak transcription	Gastric	stomach
29	chr12:42860800-42864600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:42861400-42864400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:42861400-42876000	Weak transcription	Lung	lung
32	chr12:42861600-42864000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:42861600-42864400	Enhancers	Fetal Brain Male	brain
34	chr12:42861600-42866200	Weak transcription	Ovary	ovary
35	chr12:42861800-42864400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:42862000-42864000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:42862000-42864000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr12:42862000-42864000	Flanking Active TSS	GM12878-XiMat	blood
39	chr12:42862000-42865800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr12:42862200-42864000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr12:42862200-42864200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:42862200-42864200	Enhancers	Fetal Brain Female	brain
43	chr12:42862200-42865200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:42862400-42864200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:42862400-42864400	Strong transcription	Fetal Lung	lung
46	chr12:42862400-42864400	Enhancers	Fetal Thymus	thymus
47	chr12:42862400-42864400	Strong transcription	Spleen	Spleen
48	chr12:42862400-42866000	Strong transcription	HSMMtube	muscle
49	chr12:42862400-42867200	Genic enhancers	HUVEC	blood vessel
50	chr12:42862400-42867400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links