Variant report

Variant	rs755917
Chromosome Location	chr8:95215035-95215036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GEM-1	chr8:95214701-95215280	NONHSAT127766

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10504934	0.84[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10956904	0.86[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10956905	0.97[ASN][1000 genomes]
rs10956906	0.97[ASN][1000 genomes]
rs11777372	0.97[ASN][1000 genomes]
rs11779791	0.97[ASN][1000 genomes]
rs11786049	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12114629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1350283	1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs17727794	0.97[ASN][1000 genomes]
rs1817244	0.81[CHB][hapmap]
rs1817245	0.97[ASN][1000 genomes]
rs1971965	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2005489	0.80[ASN][1000 genomes]
rs2607058	0.80[ASN][1000 genomes]
rs2613213	0.90[JPT][hapmap]
rs2613221	0.83[ASN][1000 genomes]
rs2613225	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2623155	0.83[ASN][1000 genomes]
rs2623156	0.83[ASN][1000 genomes]
rs2623157	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs34689002	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3757995	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.83[ASN][1000 genomes]
rs3886489	0.95[MEX][hapmap]
rs4587298	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55795711	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56129387	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59605341	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59773910	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60945589	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62523262	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62523265	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62523266	0.97[ASN][1000 genomes]
rs62523277	0.97[ASN][1000 genomes]
rs62523278	0.89[EUR][1000 genomes]
rs62523279	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6981215	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6989467	0.81[CHB][hapmap]
rs723360	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs7819765	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874019	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs900051	0.81[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9642922	0.97[ASN][1000 genomes]
rs9643341	0.97[ASN][1000 genomes]
rs978639	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024907	chr8:95188944-95296378	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv539677	chr8:95188944-95296378	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1022972	chr8:95189085-95245392	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1024893	chr8:95189085-95293557	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv518636	chr8:95196794-95233336	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv539678	chr8:95197036-95225644	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1030292	chr8:95198982-95231692	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv522024	chr8:95199215-95232449	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1020665	chr8:95199302-95232062	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1022489	chr8:95212660-95273564	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv539679	chr8:95212660-95273564	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1035036	chr8:95213244-95283014	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs755917	KIAA1429	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95212200-95218000	Weak transcription	Colonic Mucosa	Colon
2	chr8:95212400-95217000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr8:95212600-95220600	Weak transcription	Stomach Mucosa	stomach
4	chr8:95213000-95215800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr8:95213800-95218000	Weak transcription	A549	lung
6	chr8:95214200-95215200	Strong transcription	Fetal Intestine Large	intestine
7	chr8:95214200-95215200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr8:95214400-95215200	Strong transcription	Fetal Intestine Small	intestine
9	chr8:95214400-95215600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr8:95214800-95215200	Enhancers	Small Intestine	intestine
11	chr8:95214800-95216200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr8:95215000-95215800	Enhancers	Cortex derived primary cultured neurospheres	brain

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