Variant report

Variant	rs10062340
Chromosome Location	chr5:58432413-58432414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10055095	0.96[ASN][1000 genomes]
rs10062397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1038080	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654485	0.88[CEU][hapmap]
rs13176291	0.80[CHB][hapmap]
rs1551939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559251	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs16877156	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2409628	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33927508	0.88[CEU][hapmap]
rs35728243	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4700321	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6450506	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs6450507	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs716908	0.86[CHB][hapmap]
rs7707392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730574	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs922435	0.84[ASN][1000 genomes]
rs922437	0.84[ASN][1000 genomes]
rs9292195	0.83[MEX][hapmap]
rs997421	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv881702	chr5:58432413-58474854	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10062340	KIF2A	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58424000-58439800	Weak transcription	Small Intestine	intestine
2	chr5:58424000-58447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58424200-58432800	Weak transcription	Right Ventricle	heart
4	chr5:58424200-58446200	Weak transcription	Fetal Intestine Large	intestine
5	chr5:58424200-58446600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:58428800-58435800	Weak transcription	Fetal Heart	heart
8	chr5:58429800-58433800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:58429800-58447200	Weak transcription	Left Ventricle	heart
10	chr5:58430000-58432600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:58430000-58434400	Weak transcription	Psoas Muscle	Psoas
12	chr5:58430000-58437000	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:58430000-58442600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:58430400-58432600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:58430600-58432600	Enhancers	A549	lung
16	chr5:58431000-58432800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:58431000-58440000	Weak transcription	Fetal Lung	lung
18	chr5:58431200-58435200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr5:58431200-58437400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:58432200-58435400	Enhancers	Hela-S3	cervix

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