Variant report

Variant	rs6670818
Chromosome Location	chr1:169869344-169869345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169866713..169870686-chr1:169874035..169877977,4	K562	blood:
2	chr1:169857692..169860981-chr1:169868132..169871394,3	K562	blood:
3	chr1:169867701..169870686-chr1:169875443..169877977,2	K562	blood:
4	chr1:169844264..169846612-chr1:169869148..169870658,2	MCF-7	breast:
5	chr1:169863360..169865846-chr1:169867336..169869423,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10733054	0.96[CEU][hapmap];0.80[TSI][hapmap]
rs10737549	0.95[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs10800479	0.93[EUR][1000 genomes]
rs10800480	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10800481	0.93[EUR][1000 genomes]
rs10800483	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs10800485	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10800486	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10919239	0.95[CEU][hapmap];0.80[TSI][hapmap]
rs10919245	0.93[EUR][1000 genomes]
rs10919248	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10919251	0.93[EUR][1000 genomes]
rs10919263	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12133843	0.96[CEU][hapmap];0.89[MEX][hapmap];0.92[EUR][1000 genomes]
rs12724797	0.83[CEU][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1534904	0.82[ASW][hapmap]
rs1883436	0.92[EUR][1000 genomes]
rs1883437	0.88[AMR][1000 genomes]
rs2050651	0.82[ASW][hapmap];0.92[LWK][hapmap];0.80[MEX][hapmap]
rs2056980	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2056981	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs2179396	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2281039	0.93[EUR][1000 genomes]
rs2294322	0.93[EUR][1000 genomes]
rs2420512	0.93[EUR][1000 genomes]
rs2420514	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2485462	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2491087	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2491088	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2750014	0.85[MEX][hapmap];0.80[TSI][hapmap]
rs2750016	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2750020	0.84[EUR][1000 genomes]
rs2806382	0.82[EUR][1000 genomes]
rs2806386	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2806388	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2806393	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2901179	1.00[YRI][hapmap]
rs3753308	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766132	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs3766134	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs3766137	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs3766142	0.91[EUR][1000 genomes]
rs3766148	0.96[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs3766151	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3766154	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3766155	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4141917	0.83[CEU][hapmap]
rs4376791	0.91[EUR][1000 genomes]
rs4508080	1.00[CEU][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs4614317	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4615900	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs4656196	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4656721	1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs4656725	0.90[EUR][1000 genomes]
rs6427217	0.82[CEU][hapmap]
rs6427220	0.87[CEU][hapmap]
rs6427225	1.00[CEU][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs6427228	0.88[EUR][1000 genomes]
rs6656965	0.95[EUR][1000 genomes]
rs6669794	0.91[EUR][1000 genomes]
rs6671752	0.87[EUR][1000 genomes]
rs6680508	0.96[CEU][hapmap]
rs6680650	0.93[EUR][1000 genomes]
rs6682137	0.89[EUR][1000 genomes]
rs6682835	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6683056	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6702969	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs717481	0.95[EUR][1000 genomes]
rs732185	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs7521700	0.81[MEX][hapmap]
rs7525259	0.96[CEU][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs7530237	0.96[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs7545011	0.93[EUR][1000 genomes]
rs9287097	0.96[CEU][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6670818	C1orf112	cis	cerebellum	SCAN
rs6670818	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs6670818	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169867200-169869400	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr1:169868200-169869800	Enhancers	Fetal Intestine Large	intestine
3	chr1:169868400-169869400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:169868800-169869600	Enhancers	Fetal Intestine Small	intestine
5	chr1:169869000-169869400	Enhancers	HMEC	breast
6	chr1:169869000-169871600	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr1:169869200-169869400	Enhancers	Rectal Mucosa Donor 31	rectum

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