Variant report

Variant	rs1567739
Chromosome Location	chr12:39795178-39795179
allele	A/C
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	chr12:39792518..39795193-chr12:39798527..39801393,2	K562	blood:
3	chr12:39793372..39796238-chr12:39806830..39809770,2	K562	blood:
4	chr12:39788415..39791571-chr12:39793998..39797026,3	K562	blood:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10876868	0.95[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876876	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.82[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876972	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11171674	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171675	0.83[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171676	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171720	0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11171730	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11171789	0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171891	0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171901	0.86[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.83[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171938	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.81[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];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[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];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap]
rs11830643	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[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];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11836755	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12228767	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230604	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]
rs12424345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512942	0.85[ASN][1000 genomes]
rs17127019	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1828653	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]
rs1955314	0.80[ASN][1000 genomes]
rs2388320	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]
rs3736466	0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4284427	0.91[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.93[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];0.87[CHD][hapmap];1.00[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]
rs4500523	0.96[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs57756176	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57833783	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58240943	0.84[ASN][1000 genomes]
rs58613501	0.83[ASN][1000 genomes]
rs60792848	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7133376	0.94[ASW][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap]
rs7137143	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73094410	0.83[ASN][1000 genomes]
rs7316073	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs7953548	0.82[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965222	0.82[ASN][1000 genomes]
rs7968837	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.94[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	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7979444	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs958914	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1567739	KIF21A	cis	cerebellum	SCAN

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	chr12:39781400-39800200	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	chr12:39785200-39796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39785400-39796600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:39786400-39796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:39789000-39799400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:39789200-39800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:39789400-39795400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:39790000-39816200	Weak transcription	Right Ventricle	heart
13	chr12:39791800-39796200	Weak transcription	Left Ventricle	heart
14	chr12:39791800-39797800	Enhancers	Fetal Heart	heart
15	chr12:39791800-39799600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:39792000-39796800	Weak transcription	GM12878-XiMat	blood
17	chr12:39792600-39798000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:39793600-39799800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:39794200-39795400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:39794200-39795400	Weak transcription	NHEK	skin
21	chr12:39794200-39824800	Weak transcription	Right Atrium	heart
22	chr12:39795000-39795400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:39795000-39795800	Enhancers	Colon Smooth Muscle	Colon
24	chr12:39795000-39796200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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