Variant report

Variant	rs10069540
Chromosome Location	chr5:150942179-150942180
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:150942025..150944523-chr5:150961662..150964571,2	K562	blood:
2	chr5:150939504..150942408-chr5:150945212..150947600,2	MCF-7	breast:
3	chr5:150933953..150936226-chr5:150941566..150943074,2	K562	blood:
4	chr5:150933361..150936096-chr5:150939863..150943066,3	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10039591	0.88[ASN][1000 genomes]
rs10044120	0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10052817	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10054406	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060613	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10060662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10069901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071034	0.90[ASN][1000 genomes]
rs10072841	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10074454	0.86[ASN][1000 genomes]
rs10079712	0.90[ASN][1000 genomes]
rs10085060	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11746958	0.90[ASN][1000 genomes]
rs11750312	0.90[ASN][1000 genomes]
rs12055366	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs13158643	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159039	0.81[CEU][hapmap]
rs13166858	0.90[ASN][1000 genomes]
rs13167092	0.90[ASN][1000 genomes]
rs13187324	0.90[ASN][1000 genomes]
rs1432862	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1432866	0.90[ASN][1000 genomes]
rs1541909	0.88[ASN][1000 genomes]
rs1835944	0.90[ASN][1000 genomes]
rs2163769	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304053	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2304054	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[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]
rs28449749	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34335300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34346367	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35211425	0.87[ASN][1000 genomes]
rs35908499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35957412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734055	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734057	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734058	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3734059	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734060	0.83[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4314387	0.90[ASN][1000 genomes]
rs4320248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4376256	0.90[ASN][1000 genomes]
rs4416593	0.90[ASN][1000 genomes]
rs4416594	0.90[ASN][1000 genomes]
rs4416595	0.89[ASN][1000 genomes]
rs4452546	0.90[ASN][1000 genomes]
rs6859217	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6878528	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6878532	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6878556	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6878627	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6880902	0.87[ASN][1000 genomes]
rs6883153	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6883216	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7709576	0.88[ASN][1000 genomes]
rs7710596	0.90[ASN][1000 genomes]
rs7719117	0.90[ASN][1000 genomes]
rs7726769	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7727173	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7732813	0.89[ASN][1000 genomes]
rs7737011	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7737419	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9324698	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9324699	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9324700	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9918229	0.90[ASN][1000 genomes]
rs9918283	0.90[ASN][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	esv20633	chr5:150941705-150955343	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10069540	PPARGC1B	cis	cerebellum	SCAN
rs10069540	CNOT8	cis	parietal	SCAN
rs10069540	PCYOX1L	cis	parietal	SCAN
rs10069540	JAKMIP2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:150908200-150948000	Strong transcription	HMEC	breast
2	chr5:150908400-150944000	Strong transcription	NHEK	skin
3	chr5:150909200-150942400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:150911600-150942800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:150918200-150945400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:150931000-150942800	Weak transcription	Brain Angular Gyrus	brain
7	chr5:150934200-150949600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:150937000-150948600	Weak transcription	Right Atrium	heart
9	chr5:150937600-150948600	Weak transcription	Adipose Nuclei	Adipose
10	chr5:150940800-150942600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:150940800-150943200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr5:150941400-150942200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr5:150941400-150942600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:150941600-150942200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:150941800-150942200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:150941800-150942200	Genic enhancers	Esophagus	oesophagus

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