Variant report

Variant	rs4380891
Chromosome Location	chr8:10338924-10338925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRSS55-1	chr8:10338692-10338976	ENSG00000253641
2	lnc-RP1L1-2	chr8:10338909-10340741	NONHSAT124998

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11250019	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11250020	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11250024	0.83[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs11774920	0.83[AMR][1000 genomes]
rs11775128	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11780245	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11783249	0.81[CEU][hapmap]
rs11787130	0.88[EUR][1000 genomes]
rs11987962	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12216792	0.83[AMR][1000 genomes]
rs12216837	0.83[AMR][1000 genomes]
rs12543028	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12546721	0.83[AMR][1000 genomes]
rs13266986	0.83[CEU][hapmap]
rs13282174	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1986358	0.82[AMR][1000 genomes]
rs34448335	0.88[EUR][1000 genomes]
rs34460626	0.86[EUR][1000 genomes]
rs35386136	0.85[EUR][1000 genomes]
rs35403599	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35943454	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4128655	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4273819	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs4295624	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4348450	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs4361726	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4392860	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4523215	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4531008	0.81[ASN][1000 genomes]
rs4532561	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4840487	0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs4841363	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs56941638	0.88[EUR][1000 genomes]
rs57127715	0.87[EUR][1000 genomes]
rs57759396	0.83[AMR][1000 genomes]
rs57963113	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58044386	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59681223	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6980700	0.82[AMR][1000 genomes]
rs6984615	0.81[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs6995374	0.82[AMR][1000 genomes]
rs7007383	0.86[AMR][1000 genomes]
rs71516581	0.86[EUR][1000 genomes]
rs7357591	0.81[ASN][1000 genomes]
rs7821267	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7821273	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7842925	0.85[AMR][1000 genomes];0.96[EUR][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	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv890349	chr8:10294330-10355302	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1019090	chr8:10303099-10369061	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1024976	chr8:10303099-10385361	Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1030856	chr8:10303099-10439064	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv890350	chr8:10305317-10346588	Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv610268	chr8:10331636-10486652	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4380891	FLJ10661	cis	cerebellum	SCAN
rs4380891	CLDN23	cis	multi-tissue	Pritchard
rs4380891	PPP1R3B	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10329000-10345600	Weak transcription	Brain Hippocampus Middle	brain
2	chr8:10329200-10339200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr8:10329200-10340400	Weak transcription	Brain Angular Gyrus	brain
4	chr8:10329200-10342200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr8:10331000-10341000	Weak transcription	Spleen	Spleen
6	chr8:10331000-10341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr8:10331200-10342800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr8:10332400-10339400	Weak transcription	Ovary	ovary
9	chr8:10332600-10340400	Weak transcription	Gastric	stomach
10	chr8:10332800-10339800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:10332800-10344000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr8:10335200-10339800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:10335400-10342200	Strong transcription	Brain Germinal Matrix	brain
14	chr8:10335400-10355200	Weak transcription	Fetal Brain Male	brain
15	chr8:10335600-10339400	Weak transcription	Pancreas	Pancrea
16	chr8:10335600-10341200	Weak transcription	Adipose Nuclei	Adipose
17	chr8:10335800-10357600	Weak transcription	Brain Anterior Caudate	brain
18	chr8:10336200-10350200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr8:10337200-10339400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr8:10337200-10341800	Weak transcription	Lung	lung
21	chr8:10337400-10340000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr8:10337800-10339400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:10338000-10339600	Weak transcription	Fetal Brain Female	brain
24	chr8:10338000-10357600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr8:10338200-10339600	Strong transcription	Liver	Liver

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