Variant report

Variant	rs1828653
Chromosome Location	chr12:39796559-39796560
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39793686..39797447-chr12:39835348..39837306,4	MCF-7	breast:
2	chr12:39792266..39793961-chr12:39796104..39798981,2	MCF-7	breast:
3	chr12:39788415..39791571-chr12:39793998..39797026,3	K562	blood:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10876868	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876876	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876886	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876972	0.88[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11171674	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171675	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171676	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171720	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171730	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171789	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171891	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171901	0.82[ASW][hapmap];1.00[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171923	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171938	1.00[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172108	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11172120	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs11172183	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11172282	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11172492	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs11172592	0.82[CEU][hapmap];0.94[JPT][hapmap]
rs11172661	0.95[JPT][hapmap]
rs11830643	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11836755	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12228767	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230604	0.82[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424345	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1512936	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1512942	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567739	0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17127019	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1955314	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2388320	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]
rs3736466	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4284427	0.88[JPT][hapmap]
rs4320988	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs4492858	0.88[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4500523	0.83[CEU][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs57756176	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57833783	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695906	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60792848	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137143	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316073	0.90[JPT][hapmap]
rs7953548	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962283	0.87[CEU][hapmap]
rs7964447	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7968837	0.88[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs7971515	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974928	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs7979329	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7979444	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs958914	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	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
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1828653	KIF21A	cis	multi-tissue	Pritchard
rs1828653	KIF21A	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
2	chr12:39781400-39800200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:39782200-39796800	Weak transcription	A549	lung
4	chr12:39785000-39796800	Weak transcription	HMEC	breast
5	chr12:39785000-39829200	Weak transcription	K562	blood
6	chr12:39785400-39796600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:39786400-39796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:39789000-39799400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:39789200-39800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:39790000-39816200	Weak transcription	Right Ventricle	heart
11	chr12:39791800-39797800	Enhancers	Fetal Heart	heart
12	chr12:39791800-39799600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:39792000-39796800	Weak transcription	GM12878-XiMat	blood
14	chr12:39792600-39798000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:39793600-39799800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:39794200-39824800	Weak transcription	Right Atrium	heart
17	chr12:39795400-39803000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:39795400-39816600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:39795600-39799600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:39795600-39799800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:39795600-39800200	Weak transcription	Ovary	ovary
22	chr12:39796200-39796600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:39796200-39796600	Enhancers	Left Ventricle	heart
24	chr12:39796200-39805600	Weak transcription	Liver	Liver
25	chr12:39796400-39798200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:39796400-39798200	Enhancers	NHEK	skin

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