Variant report

Variant	rs6882514
Chromosome Location	chr5:61564841-61564842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61550007..61554674-chr5:61558868..61565665,10	K562	blood:
2	chr5:61557476..61560441-chr5:61562160..61565169,3	MCF-7	breast:
3	chr5:61561783..61565148-chr5:61601604..61603284,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068796	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10805379	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10939939	0.83[CEU][hapmap]
rs11738504	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11748930	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11959638	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12374477	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12374478	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12653369	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654228	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12657535	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658601	0.83[AMR][1000 genomes]
rs12659777	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs152185	0.86[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs152189	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs15807	0.91[CEU][hapmap];0.93[CHB][hapmap];0.86[GIH][hapmap]
rs168847	0.86[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs16890606	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs185048	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs247236	0.86[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs247256	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs26612	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs2961837	0.82[MEX][hapmap]
rs35009	0.90[CEU][hapmap]
rs35015	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs35016	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs4037270	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55914835	0.83[AMR][1000 genomes]
rs56095217	0.83[AMR][1000 genomes]
rs56128043	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57534920	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57835221	0.82[AMR][1000 genomes]
rs58057332	0.83[AMR][1000 genomes]
rs58266302	0.82[AMR][1000 genomes]
rs59420453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59629988	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60468842	0.82[AMR][1000 genomes]
rs60574331	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60803657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62365304	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62374961	0.80[AMR][1000 genomes]
rs6449596	0.82[AMR][1000 genomes]
rs6449597	0.83[AMR][1000 genomes]
rs6864382	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6871913	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6886044	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs6887181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6894270	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6898615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711530	0.87[CEU][hapmap]
rs7718580	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6882514	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61563200-61565000	Enhancers	Fetal Intestine Large	intestine
2	chr5:61563200-61565000	Enhancers	HMEC	breast
3	chr5:61563400-61565000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:61563400-61565200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:61563400-61566600	Weak transcription	K562	blood
6	chr5:61564000-61565000	Enhancers	Fetal Kidney	kidney
7	chr5:61564000-61565200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr5:61564000-61565200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr5:61564000-61565200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:61564200-61565000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr5:61564200-61565200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:61564200-61565200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:61564200-61565400	Enhancers	Primary T cells from cord blood	blood
14	chr5:61564200-61565400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr5:61564200-61565400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr5:61564400-61565000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:61564400-61565000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:61564400-61565000	Enhancers	A549	lung
19	chr5:61564400-61565200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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