Variant report

Variant	rs247236
Chromosome Location	chr5:61744277-61744278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10059269	0.85[ASN][1000 genomes]
rs10939939	0.89[CEU][hapmap]
rs11748930	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs11957789	0.84[AFR][1000 genomes]
rs12653369	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs12657535	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs12659777	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs152185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152189	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs152190	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs153872	0.88[ASN][1000 genomes]
rs15807	0.95[CEU][hapmap];0.90[GIH][hapmap]
rs166007	0.82[ASN][1000 genomes]
rs168847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16890606	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs183729	0.88[ASN][1000 genomes]
rs185048	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs193682	0.88[ASN][1000 genomes]
rs247256	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap]
rs26022	0.85[ASN][1000 genomes]
rs26612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs26633	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27751	0.96[GIH][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32160	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs32161	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs32179	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs32182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35009	0.95[CEU][hapmap]
rs35015	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs35016	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs39932	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700013	0.80[AMR][1000 genomes]
rs6871913	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs6882514	0.86[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs6886044	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs6893483	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6894270	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs7711530	0.83[CEU][hapmap]
rs962747	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv881729	chr5:61719506-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs247236	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61709200-61770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:61709400-61763400	Weak transcription	Aorta	Aorta
3	chr5:61709800-61746000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:61709800-61746600	Weak transcription	Fetal Thymus	thymus
5	chr5:61709800-61769000	Weak transcription	NH-A	brain
6	chr5:61709800-61809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:61710000-61746000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:61710200-61746000	Weak transcription	Primary B cells from cord blood	blood
9	chr5:61710400-61746000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:61710600-61746000	Weak transcription	A549	lung
11	chr5:61710800-61745400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:61710800-61746000	Weak transcription	HepG2	liver
13	chr5:61712000-61746000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:61714000-61746600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:61715000-61747200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:61722800-61770600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:61725800-61747200	Weak transcription	Thymus	Thymus
18	chr5:61726200-61746200	Weak transcription	HUVEC	blood vessel
19	chr5:61726400-61747200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:61728200-61746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:61728200-61752800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:61728400-61745600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:61728400-61747400	Weak transcription	Osteobl	bone
24	chr5:61728400-61748200	Weak transcription	Lung	lung
25	chr5:61728400-61752800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:61728400-61763400	Weak transcription	Pancreas	Pancrea
27	chr5:61728400-61807600	Weak transcription	Psoas Muscle	Psoas
28	chr5:61728800-61744600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:61728800-61745800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:61728800-61746800	Weak transcription	HSMMtube	muscle
31	chr5:61728800-61748200	Weak transcription	Fetal Lung	lung
32	chr5:61728800-61763000	Weak transcription	Fetal Brain Female	brain
33	chr5:61728800-61838200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:61729400-61746200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:61729600-61745600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:61729600-61746200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:61729600-61747400	Weak transcription	Right Ventricle	heart
38	chr5:61729600-61752800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:61729800-61744600	Weak transcription	Adipose Nuclei	Adipose
40	chr5:61729800-61746200	Weak transcription	HSMM	muscle
41	chr5:61730000-61748000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:61730000-61834200	Weak transcription	Gastric	stomach
43	chr5:61730200-61747200	Weak transcription	Left Ventricle	heart
44	chr5:61730200-61747600	Weak transcription	Brain Anterior Caudate	brain
45	chr5:61730800-61747200	Weak transcription	Ovary	ovary
46	chr5:61730800-61750200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:61731800-61764000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:61732000-61746000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr5:61732200-61746000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:61732200-61753200	Weak transcription	NHLF	lung

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