Variant report

Variant	rs9468322
Chromosome Location	chr6:28231243-28231244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:28231057-28231306	K562	blood:	n/a	chr6:28231133-28231144
2	FOXA1	chr6:28230962-28231379	HepG2	liver:	n/a	n/a
3	TCF7L2	chr6:28231078-28232121	Hela-S3	cervix:	n/a	chr6:28231847-28231854 chr6:28231847-28231856 chr6:28231843-28231859
4	TCF7L2	chr6:28230687-28232120	HEK293	kidney:	n/a	chr6:28231847-28231854 chr6:28231847-28231856 chr6:28231843-28231859
5	CEBPB	chr6:28230965-28231322	Hela-S3	cervix:	n/a	chr6:28231133-28231144
6	CEBPB	chr6:28230967-28231311	HepG2	liver:	n/a	chr6:28231133-28231144
7	CEBPB	chr6:28231007-28231266	A549	lung:	n/a	chr6:28231133-28231144

No.	Distal block	Cell Line	Cell type
1	chr6:28108136..28111844-chr6:28229127..28232755,4	K562	blood:
2	chr6:28196925..28198715-chr6:28230690..28232627,2	K562	blood:
3	chr6:28228574..28231688-chr6:28301541..28303929,3	K562	blood:
4	chr6:28192920..28194978-chr6:28231042..28233452,2	K562	blood:
5	chr6:28230115..28232269-chr6:28300762..28302458,2	MCF-7	breast:
6	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
7	chr6:28180865..28183340-chr6:28228825..28231312,2	K562	blood:
8	chr6:28230426..28232674-chr6:28234865..28236670,2	K562	blood:

Variant related genes	Relation type
ZKSCAN4	TF binding region
ENSG00000197062	TF binding region
ENSG00000137185	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

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];0.83[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];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs4713140	0.81[GIH][hapmap];0.83[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];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295766	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295767	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];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs9380051	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9380064	0.81[GIH][hapmap];0.82[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];0.83[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]
rs9461446	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]
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];0.83[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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468325	0.88[AFR][1000 genomes];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];0.94[AFR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9468322	VCAN	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28227000-28232000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:28227000-28233800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:28227400-28234400	Weak transcription	HSMMtube	muscle
4	chr6:28227600-28231600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:28227600-28231600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:28227600-28233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:28227600-28233800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:28227600-28233800	Weak transcription	HMEC	breast
9	chr6:28227800-28231600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:28227800-28234400	Weak transcription	Right Atrium	heart
11	chr6:28228200-28234600	Weak transcription	Left Ventricle	heart
12	chr6:28228400-28231400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:28228400-28233800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:28228400-28234000	Weak transcription	Psoas Muscle	Psoas
15	chr6:28230000-28233800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:28230000-28234200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:28230400-28234600	Weak transcription	Right Ventricle	heart
18	chr6:28230800-28231600	Enhancers	Hela-S3	cervix

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