Variant report

Variant	rs2059162
Chromosome Location	chr5:61556206-61556207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61555924..61558214-chr5:61579881..61582380,2	K562	blood:
2	chr5:61555834..61558737-chr5:61608990..61611037,2	MCF-7	breast:
3	chr5:61551611..61555704-chr5:61555776..61558862,4	K562	blood:
4	chr5:61541758..61543641-chr5:61554002..61556238,2	K562	blood:
5	chr5:61553876..61556282-chr5:61576708..61578826,2	K562	blood:
6	chr5:61554817..61557688-chr5:61629619..61631265,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1108158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740652	0.83[ASN][1000 genomes]
rs11742167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11747516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11750109	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12655562	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13155253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13156073	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs13156695	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13161789	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13162519	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13162821	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13169321	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13170425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13174779	0.83[ASN][1000 genomes]
rs13176923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13178729	0.87[AMR][1000 genomes]
rs13181377	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13189446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153860	0.92[CHB][hapmap]
rs153864	1.00[CHB][hapmap]
rs153866	0.92[CHB][hapmap]
rs153869	0.90[CHB][hapmap]
rs153873	0.90[CHB][hapmap]
rs16875037	0.83[ASN][1000 genomes]
rs16890613	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16890618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16890628	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16890634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16890651	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16898838	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2063255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272291	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2441115	0.90[CHB][hapmap]
rs27090	0.90[CHB][hapmap]
rs34220654	0.83[ASN][1000 genomes]
rs34596001	0.83[ASN][1000 genomes]
rs35058	0.92[CHB][hapmap]
rs35238667	0.83[ASN][1000 genomes]
rs35311093	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35572300	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35672643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35699711	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35744020	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35746052	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35794032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35808056	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35842742	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36105063	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3776612	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3776614	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3822487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4289514	0.83[ASN][1000 genomes]
rs71617425	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71617426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71617427	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71617428	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7446543	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs814169	1.00[CHB][hapmap]
rs971965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2059162	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61552800-61556400	Weak transcription	Fetal Thymus	thymus
2	chr5:61552800-61556600	Weak transcription	Thymus	Thymus
3	chr5:61552800-61557400	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr5:61552800-61557800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr5:61553000-61556400	Weak transcription	Fetal Muscle Leg	muscle
6	chr5:61553000-61557800	Enhancers	Primary T cells from cord blood	blood
7	chr5:61553000-61557800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:61553600-61557800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr5:61554000-61557200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:61555000-61557800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr5:61555200-61559000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:61555400-61558400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr5:61555600-61556400	Enhancers	Brain Angular Gyrus	brain
14	chr5:61555600-61556400	Enhancers	Brain Cingulate Gyrus	brain
15	chr5:61555600-61556400	Enhancers	Fetal Lung	lung
16	chr5:61555600-61556600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr5:61555600-61556800	Enhancers	Pancreas	Pancrea
18	chr5:61555600-61557000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:61555600-61557200	Enhancers	K562	blood
20	chr5:61555600-61557400	Enhancers	Brain Substantia Nigra	brain
21	chr5:61555600-61557600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:61555800-61556400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr5:61555800-61556800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr5:61555800-61556800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr5:61555800-61557200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:61555800-61557400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:61555800-61557600	Enhancers	Primary hematopoietic stem cells	blood
28	chr5:61555800-61557600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr5:61555800-61557800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr5:61556000-61556800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:61556000-61557600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:61556000-61558400	Enhancers	Brain Germinal Matrix	brain
33	chr5:61556200-61556400	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr5:61556200-61556600	Active TSS	Brain Anterior Caudate	brain
35	chr5:61556200-61556800	Enhancers	Adipose Nuclei	Adipose

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