Variant report

Variant	rs12741457
Chromosome Location	chr1:217188451-217188452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11572415	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs11572427	0.93[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11572435	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577589	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11585218	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585774	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12723476	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12724974	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731437	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12738035	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12747869	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12748650	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12750129	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12756498	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12759546	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12759584	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044977	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17635718	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17636663	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17686743	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17686866	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1890555	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34056739	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34096624	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34493634	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34904258	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35185630	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35409092	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35701761	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846800	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4846801	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6604651	0.82[CHD][hapmap]
rs6681177	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6684076	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71643437	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71643439	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs867409	1.00[ASW][hapmap]
rs946438	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468149	chr1:217134966-217203091	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv549204	chr1:217134966-217203091	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1011212	chr1:217162443-217206765	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12741457	ANGEL2	cis	parietal	SCAN
rs12741457	NSL1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217157400-217194400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:217185600-217194600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:217186600-217191600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:217186600-217191800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:217188200-217190200	Weak transcription	Fetal Heart	heart

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