Variant report

Variant	rs2344396
Chromosome Location	chr5:61605567-61605568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr5:61605413-61605836	IMR90	lung:	n/a	chr5:61605751-61605765

No.	Distal block	Cell Line	Cell type
1	chr5:61604944..61606842-chr5:61609048..61611891,3	MCF-7	breast:
2	chr5:61604639..61607587-chr5:61647579..61650088,2	MCF-7	breast:
3	chr5:61592874..61595599-chr5:61604099..61606788,3	K562	blood:
4	chr5:61591991..61594374-chr5:61603392..61605599,2	K562	blood:

Variant related genes	Relation type
KIF2A	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10044843	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069745	0.83[CEU][hapmap]
rs10461472	0.88[CEU][hapmap]
rs10471545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939939	0.89[CEU][hapmap]
rs13159750	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13361143	0.88[CEU][hapmap]
rs149540	0.84[CEU][hapmap]
rs152184	0.84[CEU][hapmap]
rs152187	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs152188	0.81[EUR][1000 genomes]
rs152191	0.84[CEU][hapmap]
rs152192	0.83[CEU][hapmap]
rs152199	0.84[CEU][hapmap]
rs152206	0.80[EUR][1000 genomes]
rs152215	0.84[CEU][hapmap]
rs153857	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs153858	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs153862	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs16890622	0.88[CEU][hapmap]
rs173522	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs174647	0.88[CEU][hapmap]
rs2112884	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2289883	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs2344395	0.89[CHD][hapmap]
rs247229	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs247233	0.84[CEU][hapmap]
rs247240	0.84[CEU][hapmap]
rs247244	0.84[CEU][hapmap]
rs247245	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs247247	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs247265	0.88[CEU][hapmap]
rs247270	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[MEX][hapmap]
rs264530	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[MEX][hapmap]
rs26624	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs26625	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs26628	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs26629	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs26630	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs26637	0.84[CEU][hapmap]
rs26638	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs26645	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs26649	0.86[EUR][1000 genomes]
rs27542	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs27693	0.84[CEU][hapmap]
rs35010	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs35056	0.86[EUR][1000 genomes]
rs35057	0.83[EUR][1000 genomes]
rs35059	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs3822485	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs3846466	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs40108	0.82[EUR][1000 genomes]
rs4037273	0.83[AMR][1000 genomes]
rs4290970	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4441833	0.88[CEU][hapmap]
rs4700004	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56836756	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7702634	0.88[CEU][hapmap]
rs7707035	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs784921	0.84[CEU][hapmap]
rs9291756	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs959899	0.84[CEU][hapmap]

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
rs2344396	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603200-61629200	Weak transcription	Lung	lung
2	chr5:61603200-61629200	Weak transcription	Spleen	Spleen
3	chr5:61603400-61606800	Weak transcription	Small Intestine	intestine
4	chr5:61603400-61607400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:61603400-61625200	Weak transcription	Stomach Mucosa	stomach
6	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
7	chr5:61603600-61622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:61603600-61622400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:61603600-61629200	Weak transcription	Psoas Muscle	Psoas
10	chr5:61603800-61605600	Enhancers	Brain Substantia Nigra	brain
11	chr5:61603800-61605800	Enhancers	Brain Angular Gyrus	brain
12	chr5:61603800-61606400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:61603800-61607600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:61603800-61607800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:61603800-61609600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:61603800-61611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:61603800-61611200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:61603800-61611200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:61603800-61629200	Weak transcription	Left Ventricle	heart
20	chr5:61604000-61606200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:61604000-61606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:61604000-61606400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:61604000-61606400	Weak transcription	Fetal Lung	lung
24	chr5:61604000-61606400	Weak transcription	Osteobl	bone
25	chr5:61604000-61606800	Weak transcription	Adipose Nuclei	Adipose
26	chr5:61604000-61607400	Weak transcription	Fetal Intestine Small	intestine
27	chr5:61604000-61607400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:61604000-61607800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:61604000-61607800	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:61604000-61608000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:61604000-61611000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:61604000-61617400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:61604000-61622200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:61604000-61622200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:61604000-61622200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:61604000-61629000	Weak transcription	Thymus	Thymus
37	chr5:61604200-61606200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:61604200-61607000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:61604200-61609000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:61604200-61609000	Enhancers	Brain Anterior Caudate	brain
41	chr5:61604200-61609200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:61604200-61616800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:61604400-61605600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr5:61604400-61605600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:61604400-61605600	Strong transcription	NHEK	skin
46	chr5:61604400-61605600	Weak transcription	NHLF	lung
47	chr5:61604400-61605800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:61604400-61606000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr5:61604400-61606000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:61604400-61606000	Weak transcription	Fetal Brain Male	brain

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