Variant report

Variant	rs9393902
Chromosome Location	chr6:28137730-28137731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28129361..28132360-chr6:28134442..28137799,3	MCF-7	breast:
2	chr6:28136271..28138102-chr6:28146018..28148552,2	K562	blood:
3	chr6:28135297..28137583-chr6:28137642..28140469,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226314	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
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];0.82[ASN][1000 genomes]
rs1321504	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1321505	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1339899	0.83[TSI][hapmap]
rs13437126	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13437444	0.84[AFR][1000 genomes];0.94[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894011	0.83[TSI][hapmap]
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]
rs213241	0.83[TSI][hapmap]
rs213244	0.83[TSI][hapmap]
rs2799077	0.81[GIH][hapmap]
rs34130214	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34712084	0.88[AFR][1000 genomes];0.97[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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.97[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];0.97[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];0.97[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];0.97[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];1.00[ASN][1000 genomes]
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];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9357064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9380031	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs9380032	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9380051	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]
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];0.96[ASN][1000 genomes]
rs9380069	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs9393882	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9393889	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];0.97[ASN][1000 genomes]
rs9461439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.97[ASN][1000 genomes]
rs9468300	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9468301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs9468342	1.00[YRI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9393902	VCAN	trans	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28129800-28138800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28129800-28142200	Weak transcription	Aorta	Aorta
3	chr6:28129800-28145400	Weak transcription	Brain Angular Gyrus	brain
4	chr6:28130000-28139000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:28130000-28141400	Weak transcription	Right Ventricle	heart
6	chr6:28130000-28142600	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:28130200-28138600	Weak transcription	Primary B cells from cord blood	blood
8	chr6:28130200-28138600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:28130200-28139200	Weak transcription	Fetal Brain Female	brain
10	chr6:28130200-28140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:28130200-28141800	Weak transcription	Fetal Kidney	kidney
12	chr6:28130200-28142800	Weak transcription	Left Ventricle	heart
13	chr6:28130400-28139200	Weak transcription	Adipose Nuclei	Adipose
14	chr6:28130400-28140200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:28130400-28140800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:28130400-28142600	Weak transcription	Psoas Muscle	Psoas
17	chr6:28130600-28139000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:28130600-28139200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:28130600-28139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:28130600-28139800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:28130600-28141800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:28133200-28139600	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:28133600-28140800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:28135600-28140200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:28135800-28141600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:28136400-28138000	Enhancers	K562	blood
27	chr6:28136800-28139400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr6:28137200-28138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:28137400-28137800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:28137400-28138600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:28137400-28140800	Strong transcription	Brain Cingulate Gyrus	brain

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