Variant report

Variant	rs11119328
Chromosome Location	chr1:209885318-209885319
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209877047..209878564-chr1:209885238..209887392,2	K562	blood:

Variant related genes	Relation type
ENSG00000117594	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1000282	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1000283	0.81[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10863783	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863785	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11119327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119330	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119331	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119332	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11119336	0.84[AMR][1000 genomes]
rs11119340	0.87[MEX][hapmap]
rs11119341	0.80[MEX][hapmap]
rs11485195	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11487866	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806703	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811440	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034758	0.80[AMR][1000 genomes]
rs12059226	0.86[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12060420	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12060922	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12086634	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12090931	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094117	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116437	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12120361	0.93[GIH][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs12138452	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1415542	0.86[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474654	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474655	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17389184	0.80[MEX][hapmap]
rs17389198	0.80[AMR][1000 genomes]
rs2272867	0.81[MEX][hapmap]
rs3766619	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61820570	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672256	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs667681	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6679099	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6752	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7539852	0.86[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7548781	0.83[TSI][hapmap]
rs909710	0.87[MEX][hapmap];0.89[MKK][hapmap];0.86[AMR][1000 genomes]
rs932335	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9430012	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9430014	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9430016	0.81[CHD][hapmap]
rs9430017	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1004343	chr1:209879304-209909385	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv525445	chr1:209885318-209912593	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11119328	IRF6	cis	cerebellum	SCAN
rs11119328	ETNK2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209878600-209888200	Weak transcription	Brain Angular Gyrus	brain
2	chr1:209878800-209893400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:209881200-209886000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209881400-209887200	Weak transcription	HMEC	breast
5	chr1:209882200-209887000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:209882400-209887000	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:209882400-209887000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:209882600-209886800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:209883000-209887400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:209883200-209886000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:209884000-209886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:209884000-209889000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:209884400-209887400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:209884600-209886000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:209885000-209886200	Weak transcription	NHEK	skin
16	chr1:209885000-209886600	Weak transcription	Liver	Liver
17	chr1:209885000-209887200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:209885000-209888200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:209885200-209886400	Enhancers	HUVEC	blood vessel

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