Variant report

Variant	rs6427229
Chromosome Location	chr1:169879547-169879548
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	chr1:169861017..169866202-chr1:169878725..169885490,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10159425	0.88[EUR][1000 genomes]
rs10489170	0.91[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs10489177	0.91[MEX][hapmap]
rs10800477	0.91[MEX][hapmap]
rs10800494	0.80[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap]
rs10800495	0.80[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap]
rs10919260	0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10919270	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10919271	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10919272	0.89[ASW][hapmap];0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10919284	0.81[CHB][hapmap]
rs11803298	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs11804170	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12049325	0.84[JPT][hapmap]
rs12123693	0.80[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap]
rs12124607	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs12126204	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs12128754	0.91[MEX][hapmap]
rs12135826	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12137754	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs12138675	0.91[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12146137	0.80[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap]
rs12401321	0.91[EUR][1000 genomes]
rs12401338	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12757747	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360293	0.80[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap]
rs35275808	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35414012	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35688996	0.86[JPT][hapmap]
rs6427233	0.80[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap]
rs6657512	0.80[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap]
rs6658548	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6670191	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs6679646	0.91[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs6688806	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74122428	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7514634	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs7521273	0.92[GIH][hapmap]
rs7533194	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6427229	CREG1	cis	cerebellum	SCAN
rs6427229	C1orf156	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169872800-169887800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:169875800-169889800	Weak transcription	Fetal Brain Female	brain
3	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
4	chr1:169876600-169883000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:169876800-169883400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:169877000-169884000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:169877600-169889800	Weak transcription	Lung	lung
8	chr1:169878400-169882400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:169878400-169892200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:169878400-169895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:169878600-169880000	Enhancers	GM12878-XiMat	blood
13	chr1:169878600-169883600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:169878600-169895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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