Variant report

Variant	rs12230604
Chromosome Location	chr12:39790443-39790444
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39788415..39791571-chr12:39793998..39797026,3	K562	blood:

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

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

rs_ID	r²[population]
rs10876868	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876876	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11171674	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171675	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171676	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171720	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171730	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171789	0.88[ASW][hapmap];0.95[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];0.97[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171891	0.88[ASW][hapmap];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];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171901	1.00[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171938	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs11172183	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11172282	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[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];0.85[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];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[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];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567739	0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1828653	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]
rs1955314	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2388320	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]
rs3736466	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[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];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4500523	0.83[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs57756176	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57833783	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695906	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60792848	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137143	0.88[ASW][hapmap];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];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316073	0.90[JPT][hapmap]
rs7953548	0.94[AMR][1000 genomes];0.98[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	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[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	0.94[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];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs958914	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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
rs12230604	KIF21A	cis	cerebellum	SCAN
rs12230604	KIF21A	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
2	chr12:39767600-39791400	Weak transcription	GM12878-XiMat	blood
3	chr12:39781200-39791400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:39781400-39800200	Weak transcription	Brain Angular Gyrus	brain
5	chr12:39782200-39796800	Weak transcription	A549	lung
6	chr12:39785000-39791200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:39785000-39796800	Weak transcription	HMEC	breast
8	chr12:39785000-39829200	Weak transcription	K562	blood
9	chr12:39785200-39796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:39785400-39796600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:39786400-39791200	Weak transcription	Psoas Muscle	Psoas
12	chr12:39786400-39796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:39786600-39791400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:39788000-39791400	Weak transcription	Gastric	stomach
15	chr12:39788400-39791400	Enhancers	Fetal Heart	heart
16	chr12:39789000-39799400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:39789200-39800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:39789400-39791400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:39789400-39795400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:39790000-39791400	Weak transcription	Left Ventricle	heart
21	chr12:39790000-39793000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:39790000-39793400	Weak transcription	Right Atrium	heart
23	chr12:39790000-39816200	Weak transcription	Right Ventricle	heart
24	chr12:39790200-39791400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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