Variant report

Variant	rs1792624
Chromosome Location	chr11:93921810-93921811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR83-5	chr11:93921615-93922163	NONHSAT023708

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10444216	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1046805	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1046812	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1070	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10765655	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10765656	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10831170	0.82[EUR][1000 genomes]
rs11020675	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11605491	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1540177	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16920011	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1789650	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1789653	0.83[AMR][1000 genomes]
rs1789655	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792634	0.84[CEU][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs1857681	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1893808	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1893809	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3020014	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3020015	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3020017	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs625080	0.85[AMR][1000 genomes]
rs659288	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898184	chr11:93741612-93969726	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1046092	chr11:93833446-93964452	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv898185	chr11:93851048-93927529	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv469980	chr11:93864321-93962121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv468795	chr11:93864321-93964917	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv555966	chr11:93864321-93964917	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1038294	chr11:93918837-93982605	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv975970	chr11:93920948-93922138	Weak transcription Enhancers Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1792624	C11orf54	cis	parietal	SCAN
rs1792624	KDM4D	cis	parietal	SCAN
rs1792624	PANX1	cis	parietal	SCAN
rs1792624	PANX1	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93913600-93929400	Weak transcription	Gastric	stomach
2	chr11:93914800-93926200	Weak transcription	Esophagus	oesophagus
3	chr11:93914800-93926200	Weak transcription	Spleen	Spleen
4	chr11:93915600-93929400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:93916400-93922000	Weak transcription	Brain Germinal Matrix	brain
6	chr11:93916800-93926200	Weak transcription	HMEC	breast
7	chr11:93917200-93926200	Weak transcription	NHEK	skin
8	chr11:93917400-93922000	Weak transcription	Lung	lung
9	chr11:93917600-93923000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:93917600-93925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:93917600-93934200	Weak transcription	Fetal Intestine Small	intestine
12	chr11:93917800-93926400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:93918000-93925600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:93919200-93922200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:93919200-93925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:93919400-93925400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:93919400-93925600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:93919400-93925600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:93919400-93926000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:93919400-93926200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:93919600-93926400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:93920000-93922000	Weak transcription	Fetal Intestine Large	intestine
23	chr11:93920000-93925800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:93920000-93926600	Weak transcription	Fetal Brain Female	brain
25	chr11:93920200-93925600	Weak transcription	NHLF	lung
26	chr11:93920200-93928000	Weak transcription	HSMMtube	muscle
27	chr11:93920400-93924400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:93920400-93925600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr11:93920400-93925600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:93920400-93925600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:93920400-93925600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:93920400-93925600	Weak transcription	NHDF-Ad	bronchial
33	chr11:93920400-93926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:93920400-93926200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:93920400-93929400	Weak transcription	Pancreas	Pancrea
36	chr11:93920400-93933000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:93920400-93937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:93920600-93925600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:93920600-93926600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:93920600-93927800	Weak transcription	Aorta	Aorta
41	chr11:93921200-93926000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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