Variant report

Variant	rs11102628
Chromosome Location	chr1:113960583-113960584
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	chr1:113950704..113953604-chr1:113960173..113962472,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10458458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10458459	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.99[ASN][1000 genomes]
rs10857994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10857996	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11102627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102636	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11102637	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11102638	0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs11102639	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];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11102641	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11102647	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];0.95[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs1112085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1112543	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[ASN][1000 genomes]
rs12021783	0.93[ASN][1000 genomes]
rs12022213	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs12022849	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs12023641	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs12024139	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs12024428	0.91[ASN][1000 genomes]
rs12026682	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs12027235	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12029305	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12030900	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12032395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12034178	0.99[ASN][1000 genomes]
rs12038473	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs12039669	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12039944	0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs12044485	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12045148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12045559	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12046451	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12049093	0.87[ASN][1000 genomes]
rs12049447	0.81[CHB][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs12567622	0.87[ASN][1000 genomes]
rs12568854	0.86[ASN][1000 genomes]
rs1418607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1539411	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs1573996	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs1936927	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs1936928	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs2027536	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2027537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28661018	0.84[EUR][1000 genomes]
rs4838988	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs4839320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[ASN][1000 genomes]
rs4839323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs4839324	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs55737954	0.93[ASN][1000 genomes]
rs6688827	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72687924	0.99[ASN][1000 genomes]
rs9787276	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11102628	MAGI3	cis	cerebellum	SCAN
rs11102628	AFARP1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113937600-113963400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:113940200-113987000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:113948000-113969800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:113949800-113972200	Weak transcription	Aorta	Aorta
5	chr1:113951200-113962200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:113953800-113960600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:113958400-113963400	Weak transcription	A549	lung
8	chr1:113958400-113972200	Weak transcription	Ovary	ovary
9	chr1:113959400-113965000	Weak transcription	Liver	Liver
10	chr1:113959600-113964400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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