Variant report

Variant	rs11779308
Chromosome Location	chr8:48102987-48102988
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	chr8:48102394..48104985-chr8:48106310..48110221,3	MCF-7	breast:
2	chr8:48099672..48101533-chr8:48102749..48105335,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-1134I14.8.1-1	chr8:48102395-48104885	ENSG00000255366.1
2	lnc-RP11-1134I14.8.1-1	chr8:48102596-48104139	NONHSAT126436
3	lnc-RP11-1134I14.8.1-1	chr8:48100930-48104439	NONHSAT126435

Variant related genes	Relation type
ENSG00000253817	Chromatin interaction
ENSG00000254348	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10086987	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10102598	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10808752	0.80[EUR][1000 genomes]
rs10957074	0.80[EUR][1000 genomes]
rs11778117	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11779423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781727	0.80[EUR][1000 genomes]
rs11782287	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11783141	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs12541086	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs12543823	0.81[EUR][1000 genomes]
rs12550067	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12682269	0.81[EUR][1000 genomes]
rs13259872	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[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13273902	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2087656	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2355357	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34099416	0.80[EUR][1000 genomes]
rs35424826	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35931929	0.90[ASN][1000 genomes]
rs36103744	0.82[EUR][1000 genomes]
rs4242439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388466	0.96[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs4495437	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498545	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4872957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873102	0.81[EUR][1000 genomes]
rs56099826	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6472229	0.85[EUR][1000 genomes]
rs6990123	1.00[ASW][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs7016791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7819806	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7826284	0.80[EUR][1000 genomes]
rs7839134	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs902619	0.92[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025638	chr8:47361534-48176434	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv530881	chr8:47456285-48129198	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1020467	chr8:47456484-48174712	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv539589	chr8:47456484-48174712	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv1028036	chr8:47531749-48256108	Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1019289	chr8:47536056-48251883	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv539591	chr8:47536056-48251883	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv530882	chr8:47620846-48223868	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv1015347	chr8:47698082-48318579	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv539593	chr8:47698082-48318579	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv890847	chr8:47937950-48124855	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv916549	chr8:47982642-48223882	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv1031982	chr8:47997015-48110595	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11779308	SNAI2	cis	cerebellum	SCAN
rs11779308	KIAA0146	cis	parietal	SCAN
rs11779308	MCM4	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48101000-48103200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:48101000-48105600	Weak transcription	Ovary	ovary
3	chr8:48101000-48116000	Weak transcription	Gastric	stomach
4	chr8:48101200-48103600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:48101200-48103600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr8:48101200-48103600	Weak transcription	Osteobl	bone
7	chr8:48101200-48103800	Weak transcription	NHDF-Ad	bronchial
8	chr8:48101200-48105600	Weak transcription	Spleen	Spleen
9	chr8:48101200-48109600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr8:48101200-48110800	Weak transcription	Aorta	Aorta
11	chr8:48101200-48111600	Weak transcription	Right Atrium	heart
12	chr8:48101200-48115000	Weak transcription	Pancreas	Pancrea
13	chr8:48101400-48105000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:48101800-48105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr8:48102000-48103200	Weak transcription	Fetal Brain Female	brain
16	chr8:48102400-48103000	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr8:48102400-48103800	Enhancers	Brain Hippocampus Middle	brain
18	chr8:48102400-48103800	Enhancers	Brain Substantia Nigra	brain
19	chr8:48102600-48103000	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr8:48102600-48103000	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr8:48102600-48103200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr8:48102600-48104000	Enhancers	Fetal Brain Male	brain
23	chr8:48102800-48103000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr8:48102800-48103200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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