Variant report

Variant	rs2388320
Chromosome Location	chr12:39781239-39781240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39779513..39783139-chr12:39785165..39787752,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10876868	0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876876	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876972	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11171674	0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171675	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171676	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171720	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11171730	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11171789	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171891	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171901	0.86[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171938	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172108	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs11172120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11172183	0.86[CEU][hapmap];0.94[JPT][hapmap]
rs11172282	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs11172492	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11172592	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs11172661	0.94[ASW][hapmap];0.87[CEU][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap]
rs11830643	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11836755	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12228767	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230604	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12424345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512942	0.85[ASN][1000 genomes]
rs1567739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127019	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1828653	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1955314	0.80[ASN][1000 genomes]
rs3736466	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4284427	0.91[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap]
rs4320988	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4492858	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4500523	0.96[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs57756176	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57833783	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58240943	0.84[ASN][1000 genomes]
rs58613501	0.83[ASN][1000 genomes]
rs60792848	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7137143	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73094410	0.83[ASN][1000 genomes]
rs7316073	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs7953548	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7962283	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs7964447	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965222	0.82[ASN][1000 genomes]
rs7968837	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7971515	0.87[ASN][1000 genomes]
rs7974928	0.84[CEU][hapmap];0.80[MEX][hapmap]
rs7979329	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7979444	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs958914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[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	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2388320	KIF21A	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39757000-39784600	Weak transcription	Brain Germinal Matrix	brain
2	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
3	chr12:39763000-39781400	Weak transcription	A549	lung
4	chr12:39767400-39784800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:39767600-39791400	Weak transcription	GM12878-XiMat	blood
6	chr12:39767800-39784800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:39776400-39783200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:39776600-39783800	Weak transcription	HMEC	breast
9	chr12:39777000-39783200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:39778800-39786000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:39778800-39787200	Weak transcription	Right Ventricle	heart
12	chr12:39779000-39782400	Enhancers	Fetal Heart	heart
13	chr12:39779000-39786000	Weak transcription	Left Ventricle	heart
14	chr12:39779200-39782400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:39779200-39786200	Weak transcription	Psoas Muscle	Psoas
16	chr12:39780200-39781600	Enhancers	Brain Substantia Nigra	brain
17	chr12:39780200-39781800	Enhancers	Brain Hippocampus Middle	brain
18	chr12:39780200-39787400	Weak transcription	Liver	Liver
19	chr12:39780400-39782000	Enhancers	Brain Anterior Caudate	brain
20	chr12:39780400-39789800	Weak transcription	HepG2	liver
21	chr12:39780600-39781600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr12:39780600-39781600	Enhancers	Brain Cingulate Gyrus	brain
23	chr12:39780600-39781800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:39780800-39782000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:39781000-39781600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr12:39781000-39781600	Enhancers	Right Atrium	heart
27	chr12:39781000-39782400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:39781200-39781400	Enhancers	Brain Angular Gyrus	brain
29	chr12:39781200-39791400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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