Variant report

Variant	rs595283
Chromosome Location	chr1:120247887-120247888
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120238812..120241117-chr1:120246853..120248375,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1163251	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2764886	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs477992	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs478093	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs478450	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs483180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs483360	0.82[EUR][1000 genomes]
rs487081	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs487884	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs496195	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs496198	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs511059	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs514491	0.85[CEU][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs517533	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs532303	0.96[ASN][1000 genomes]
rs539708	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs541503	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561931	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs594400	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs597308	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs598685	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs606312	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs611365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612430	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs616111	0.93[CHD][hapmap]
rs627707	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs629735	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs637868	0.86[JPT][hapmap]
rs639216	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs639761	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs640195	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs658442	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs660073	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662243	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs662602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs666930	0.86[JPT][hapmap]
rs677277	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs839600	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs839605	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs839608	0.84[EUR][1000 genomes]
rs866321	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs595283	C1orf161	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120244800-120254200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:120247000-120251600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:120247000-120251600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:120247800-120248000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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