Variant report

Variant	rs12654228
Chromosome Location	chr5:61587900-61587901
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10805379	0.86[AMR][1000 genomes]
rs1085103	0.81[EUR][1000 genomes]
rs10939939	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11738504	0.88[AMR][1000 genomes]
rs11748930	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11952777	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11957789	0.87[EUR][1000 genomes]
rs11959638	0.90[AMR][1000 genomes]
rs12374477	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12374478	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12653369	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12657535	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12658601	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12659777	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs152189	0.85[EUR][1000 genomes]
rs15807	0.85[EUR][1000 genomes]
rs166008	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs166009	0.85[EUR][1000 genomes]
rs16890606	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16890659	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs185048	0.80[EUR][1000 genomes]
rs247219	0.84[EUR][1000 genomes]
rs247224	0.82[EUR][1000 genomes]
rs247226	0.81[EUR][1000 genomes]
rs247256	0.80[EUR][1000 genomes]
rs247263	0.80[EUR][1000 genomes]
rs247271	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs247272	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs247274	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3213940	0.87[EUR][1000 genomes]
rs35008	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35009	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35014	0.80[EUR][1000 genomes]
rs35016	0.82[EUR][1000 genomes]
rs4037270	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs464058	0.82[EUR][1000 genomes]
rs55914835	0.84[AMR][1000 genomes]
rs56095217	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56128043	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57534920	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57835221	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58057332	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58266302	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59420453	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59629988	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60468842	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60574331	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60803657	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62365304	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62374960	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62374961	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6449596	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6449597	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6864382	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871913	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6882514	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6886044	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6887181	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6894270	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6898615	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7704066	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7718580	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs784900	0.85[EUR][1000 genomes]
rs784901	0.82[EUR][1000 genomes]
rs784902	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv2755585	chr5:61535831-61618595	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12654228	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61582800-61592600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:61583200-61589000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:61583400-61592600	Weak transcription	Primary T cells from cord blood	blood
4	chr5:61583800-61588200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:61586600-61589000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr5:61587000-61588200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr5:61587000-61589000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:61587000-61589800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:61587200-61588200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:61587200-61588400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:61587200-61589000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr5:61587400-61589000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr5:61587400-61589200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr5:61587800-61588600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:61587800-61588800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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