Variant report

Variant	rs9488340
Chromosome Location	chr6:114508475-114508476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:62502076..62503847-chr6:114506074..114508733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108654	Chromatin interaction
ENSG00000258890	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10782179	0.90[ASN][1000 genomes]
rs13207255	0.84[ASN][1000 genomes]
rs1401774	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519690	0.87[ASN][1000 genomes]
rs2139414	0.88[ASN][1000 genomes]
rs2349211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34481741	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4945991	0.84[GIH][hapmap]
rs4945993	0.90[ASN][1000 genomes]
rs6915954	0.90[ASN][1000 genomes]
rs6928606	0.90[ASN][1000 genomes]
rs6936717	0.90[ASN][1000 genomes]
rs7746324	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7751951	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs7766866	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs925981	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs925982	0.90[ASN][1000 genomes]
rs925983	0.90[ASN][1000 genomes]
rs928606	0.90[ASN][1000 genomes]
rs9320481	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs9320482	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs9320483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9320486	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372389	0.89[ASN][1000 genomes]
rs9372390	0.90[ASN][1000 genomes]
rs9372391	0.82[ASN][1000 genomes]
rs9374441	0.90[ASN][1000 genomes]
rs9374443	0.90[ASN][1000 genomes]
rs9387194	0.89[ASN][1000 genomes]
rs9387195	0.91[ASN][1000 genomes]
rs9387196	0.90[ASN][1000 genomes]
rs9400698	0.89[ASN][1000 genomes]
rs9400699	0.88[ASN][1000 genomes]
rs9400700	0.90[ASN][1000 genomes]
rs9400701	0.90[ASN][1000 genomes]
rs9400702	0.90[ASN][1000 genomes]
rs9400703	0.90[ASN][1000 genomes]
rs9481426	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481430	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481433	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984769	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	nsv1034897	chr6:114454186-114555679	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1029370	chr6:114471446-114566884	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv604544	chr6:114489321-114837181	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9488340	RWDD1	cis	parietal	SCAN
rs9488340	SLC16A10	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114492600-114515000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:114495400-114508600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr6:114500000-114510800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:114500000-114511000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:114501400-114515800	Weak transcription	HepG2	liver
6	chr6:114501800-114515200	Weak transcription	HSMMtube	muscle
7	chr6:114505000-114512600	Weak transcription	Psoas Muscle	Psoas

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