Variant report

Variant	rs9380051
Chromosome Location	chr6:28064091-28064092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1015075	0.95[CHD][hapmap]
rs10456362	0.81[GIH][hapmap]
rs11755032	0.83[TSI][hapmap]
rs11965538	0.81[GIH][hapmap]
rs12055625	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1321504	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1321505	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13437126	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437444	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1419183	0.81[GIH][hapmap]
rs149943	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs149990	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs1679709	0.81[GIH][hapmap]
rs16893573	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs16893601	1.00[CHB][hapmap]
rs16893735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778507	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[EUR][1000 genomes]
rs1778508	0.81[GIH][hapmap]
rs202906	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2799077	0.81[GIH][hapmap]
rs34130214	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34712084	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3734571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757188	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4713138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713139	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4713140	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6901575	0.81[GIH][hapmap]
rs6920512	0.90[YRI][hapmap]
rs735765	0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8180562	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs904142	0.90[CHD][hapmap]
rs9295765	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs9295766	0.95[EUR][1000 genomes]
rs9295767	0.95[EUR][1000 genomes]
rs9348792	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9357064	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9366717	0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs9368560	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9368561	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9380028	0.95[CHD][hapmap]
rs9380030	0.90[CHD][hapmap]
rs9380031	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs9380032	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9380064	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9380069	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs9393882	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[AMR][1000 genomes]
rs9393889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393902	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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461432	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9461439	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461446	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs9461448	0.83[TSI][hapmap]
rs9468287	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9468300	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9468301	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468321	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs9468322	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs9468325	0.95[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9380051	VCAN	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28053400-28064600	Strong transcription	Placenta	Placenta
2	chr6:28057800-28065800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:28058000-28064800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:28058200-28072200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:28058800-28072000	Weak transcription	HMEC	breast
6	chr6:28059200-28066800	Weak transcription	Esophagus	oesophagus
7	chr6:28059400-28072000	Weak transcription	Brain Substantia Nigra	brain
8	chr6:28061200-28064600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:28061400-28072000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:28062000-28064600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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