Variant report

Variant	rs4628860
Chromosome Location	chr13:51892508-51892509
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51883357..51884920-chr13:51891392..51893202,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1028727	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12860899	1.00[LWK][hapmap]
rs17194948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17195020	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2277443	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs2408363	0.86[CHB][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs56017742	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73197809	0.82[EUR][1000 genomes]
rs73197824	1.00[AFR][1000 genomes]
rs7321642	1.00[JPT][hapmap]
rs7328715	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7335122	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7335144	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7337450	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7989850	0.90[CEU][hapmap];0.93[CHD][hapmap]
rs7998084	0.90[CEU][hapmap]
rs9316541	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9316545	0.90[CEU][hapmap]
rs9526757	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs9526758	0.85[EUR][1000 genomes]
rs9526759	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9526761	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9526764	0.89[CEU][hapmap]
rs9535625	1.00[LWK][hapmap]
rs9535636	0.87[EUR][1000 genomes]
rs9535638	0.86[EUR][1000 genomes]
rs9535640	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535644	0.93[EUR][1000 genomes]
rs9535646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535655	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9535660	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9535661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9535662	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9535663	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9535665	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535670	0.90[CEU][hapmap];0.93[CHD][hapmap]
rs9535678	1.00[AFR][1000 genomes]
rs9535680	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs9535694	1.00[AFR][1000 genomes]
rs9535696	0.89[CEU][hapmap]
rs9535697	0.89[CEU][hapmap]
rs9535699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs9563046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568600	0.89[CEU][hapmap]
rs9568603	0.90[CEU][hapmap]
rs9568612	0.90[CEU][hapmap]
rs9634842	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4628860	CKAP2	cis	parietal	SCAN
rs4628860	NUDT15	cis	cerebellum	SCAN
rs4628860	HNRNPA1L2	cis	cerebellum	SCAN
rs4628860	ITM2B	cis	cerebellum	SCAN
rs4628860	INTS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51867600-51910800	Weak transcription	Pancreas	Pancrea
2	chr13:51889000-51892600	Enhancers	Osteobl	bone
3	chr13:51889000-51892800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:51889200-51892600	Enhancers	Muscle Satellite Cultured Cells	--
5	chr13:51889200-51892600	Enhancers	NH-A	brain
6	chr13:51889200-51892600	Enhancers	NHDF-Ad	bronchial
7	chr13:51889400-51901200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr13:51889800-51896200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr13:51890000-51893600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr13:51890000-51893800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr13:51890000-51897200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:51890000-51899200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr13:51890000-51904800	Weak transcription	Right Atrium	heart
14	chr13:51890200-51893200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr13:51890200-51895400	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:51890200-51896200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:51890200-51897400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr13:51890200-51899400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr13:51890400-51895600	Weak transcription	Brain Anterior Caudate	brain
20	chr13:51890400-51896200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr13:51890600-51898400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:51891000-51892800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:51892200-51897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:51892400-51897200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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