Variant report

Variant	rs12023641
Chromosome Location	chr1:113951107-113951108
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113950704..113953604-chr1:113960173..113962472,2	K562	blood:
2	chr1:113943430..113947212-chr1:113950458..113953796,3	K562	blood:
3	chr1:113932138..113934222-chr1:113949654..113952724,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10458458	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10458459	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857994	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11102627	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]
rs11102628	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]
rs11102630	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11102636	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11102637	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11102638	1.00[ASW][hapmap];0.93[CEU][hapmap];0.89[CHB][hapmap];0.94[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];0.80[EUR][1000 genomes]
rs11102639	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs11102640	0.80[EUR][1000 genomes]
rs11102641	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11102644	0.80[EUR][1000 genomes]
rs11102647	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs1112085	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112543	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12021783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022213	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[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[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12022849	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[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[AFR][1000 genomes]
rs12024139	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.91[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[AFR][1000 genomes]
rs12024428	0.99[ASN][1000 genomes]
rs12025806	0.80[EUR][1000 genomes]
rs12026005	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12026682	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[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[AFR][1000 genomes]
rs12029305	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12030900	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032395	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12033666	0.80[EUR][1000 genomes]
rs12034178	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12038473	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[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[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12038754	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12038879	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12039226	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12039603	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12039669	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12039944	1.00[ASW][hapmap];0.93[CEU][hapmap];0.89[CHB][hapmap];0.94[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[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12043827	0.87[AFR][1000 genomes]
rs12044485	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12045148	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12045559	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12046450	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12046451	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12048327	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12049093	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049447	0.86[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12567622	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568854	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418607	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539411	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573996	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes]
rs1936926	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1936927	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1936928	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs2027536	0.97[ASN][1000 genomes]
rs2027537	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359413	1.00[AFR][1000 genomes]
rs2884705	1.00[AFR][1000 genomes]
rs4838987	0.82[AMR][1000 genomes]
rs4838988	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap]
rs4839320	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4839323	0.94[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs4839324	0.93[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs55737954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66565865	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6688827	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.99[ASN][1000 genomes]
rs72687924	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72687938	0.80[EUR][1000 genomes]
rs72687939	0.80[EUR][1000 genomes]
rs72687944	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72687947	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72687948	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72687949	0.80[EUR][1000 genomes]
rs72687961	1.00[AFR][1000 genomes]
rs7413018	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9787276	0.99[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
rs12023641	CAPZA1	cis	cerebellum	SCAN
rs12023641	MAGI3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113936000-113952400	Weak transcription	Fetal Stomach	stomach
2	chr1:113937600-113963400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:113939800-113953400	Weak transcription	NHDF-Ad	bronchial
4	chr1:113940200-113952200	Weak transcription	HMEC	breast
5	chr1:113940200-113987000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:113940800-113952200	Weak transcription	Hela-S3	cervix
7	chr1:113941800-113952200	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:113944600-113958200	Weak transcription	Small Intestine	intestine
9	chr1:113944800-113952200	Weak transcription	Stomach Mucosa	stomach
10	chr1:113947000-113952400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:113948000-113953400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:113948000-113969800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:113948600-113953400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:113949800-113972200	Weak transcription	Aorta	Aorta
15	chr1:113950400-113951200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr1:113950600-113951200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:113950800-113952600	Weak transcription	Liver	Liver
18	chr1:113950800-113952600	Weak transcription	Fetal Kidney	kidney

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