Variant report

Variant	rs9382497
Chromosome Location	chr6:55361392-55361393
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10223668	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10755781	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10948936	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10948939	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10948941	0.90[CEU][hapmap];0.91[CHB][hapmap]
rs10948942	0.88[EUR][1000 genomes]
rs12193162	0.88[EUR][1000 genomes]
rs12209478	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13206666	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4144577	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4236132	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4283891	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4314500	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4360137	0.85[EUR][1000 genomes]
rs4382261	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4388287	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4404773	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4431436	0.88[EUR][1000 genomes]
rs4489157	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4496787	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4520017	0.84[EUR][1000 genomes]
rs4537142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4538708	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596474	0.88[EUR][1000 genomes]
rs4599641	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6459082	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6459083	0.96[EUR][1000 genomes]
rs6459084	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6905376	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6908139	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914087	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6925488	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6928264	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6936172	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7452170	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7740208	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7744273	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7744986	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7745290	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756201	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760065	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7761740	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7762887	0.82[ASN][1000 genomes]
rs9296793	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9370438	0.88[EUR][1000 genomes]
rs9382506	0.88[EUR][1000 genomes]
rs9464253	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9464254	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9464258	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9475314	0.82[AFR][1000 genomes]
rs9475318	0.82[AFR][1000 genomes]
rs9475333	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9475335	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9475336	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9475337	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9475339	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9475341	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475342	0.85[EUR][1000 genomes]
rs9475344	0.87[EUR][1000 genomes]
rs9791201	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9791304	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9791308	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9791360	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9885775	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470819	chr6:55236937-55368815	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1031179	chr6:55237283-55372905	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1029436	chr6:55237283-55386038	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1028560	chr6:55237723-55378113	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1024550	chr6:55237723-55387481	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv462948	chr6:55238091-55368815	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv603163	chr6:55238091-55368815	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1025276	chr6:55349638-55374178	Enhancers Weak transcription Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
10	nsv948358	chr6:55351282-55477277	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9382497	ICK	cis	cerebellum	SCAN
rs9382497	HMGCLL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55359200-55361400	Enhancers	NHEK	skin
2	chr6:55359200-55361600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:55359800-55361600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:55359800-55361600	Enhancers	HMEC	breast
5	chr6:55360400-55361400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:55360600-55361800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:55361200-55361600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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