Variant report

Variant	rs9461446
Chromosome Location	chr6:28227633-28227634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28219997..28223882-chr6:28224379..28228192,5	K562	blood:
2	chr6:28226019..28228390-chr6:28303494..28305290,2	K562	blood:
3	chr6:28217539..28222258-chr6:28227412..28230016,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187626	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10456362	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1076639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11755032	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.97[ASN][1000 genomes]
rs11965538	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13200462	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1321505	1.00[YRI][hapmap]
rs1339899	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs13437126	0.95[EUR][1000 genomes]
rs1419183	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1679709	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1679732	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16893735	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs16894011	0.83[TSI][hapmap]
rs1778507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778508	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1778511	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1936365	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs213239	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs213241	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs213243	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs213244	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs2743554	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2743555	0.91[ASN][1000 genomes]
rs2799077	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2799079	0.81[CHB][hapmap];0.89[CHD][hapmap];0.91[ASN][1000 genomes]
rs3734571	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[EUR][1000 genomes]
rs3757188	0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4713138	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs4713139	0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4713140	0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs61127718	0.86[ASN][1000 genomes]
rs68141011	0.93[ASN][1000 genomes]
rs6901575	0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6905391	0.85[ASN][1000 genomes]
rs6920512	1.00[CHB][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7740487	0.91[ASN][1000 genomes]
rs853676	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs853678	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs853679	0.82[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs853681	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs853685	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs853687	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs853688	0.80[ASN][1000 genomes]
rs853694	0.86[ASN][1000 genomes]
rs9295765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295766	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295767	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357064	0.95[EUR][1000 genomes]
rs9366717	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs9380051	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9380064	0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9380069	1.00[GIH][hapmap]
rs9393889	0.95[EUR][1000 genomes]
rs9393902	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]
rs9393908	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9461439	0.95[EUR][1000 genomes]
rs9461448	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.97[ASN][1000 genomes]
rs9461449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9468287	0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9468301	0.95[EUR][1000 genomes]
rs9468321	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]
rs9468322	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[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468325	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468342	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9468345	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9986596	0.93[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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9461446	VCAN	trans	lymphoblastoid	seeQTL
rs9461446	RP1-313I6.12	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28225800-28227800	Active TSS	Colon Smooth Muscle	Colon
2	chr6:28226200-28228200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
3	chr6:28226400-28227800	Active TSS	Brain Anterior Caudate	brain
4	chr6:28226600-28227800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:28226600-28228400	Active TSS	Psoas Muscle	Psoas
6	chr6:28226800-28227800	Bivalent/Poised TSS	Fetal Kidney	kidney
7	chr6:28227000-28228400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:28227000-28232000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:28227000-28233800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:28227200-28227800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr6:28227200-28228200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr6:28227400-28227800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:28227400-28227800	Active TSS	Right Atrium	heart
14	chr6:28227400-28234400	Weak transcription	HSMMtube	muscle
15	chr6:28227600-28227800	Enhancers	Adipose Nuclei	Adipose
16	chr6:28227600-28227800	Weak transcription	HSMM	muscle
17	chr6:28227600-28228000	Weak transcription	Left Ventricle	heart
18	chr6:28227600-28228000	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr6:28227600-28228200	Active TSS	Right Ventricle	heart
20	chr6:28227600-28228400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:28227600-28229800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:28227600-28231600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:28227600-28231600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:28227600-28233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:28227600-28233800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:28227600-28233800	Weak transcription	HMEC	breast

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