Variant report

Variant	rs10831169
Chromosome Location	chr11:93922134-93922135
allele	A/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: 47 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1014499	0.94[EUR][1000 genomes]
rs10458852	0.97[EUR][1000 genomes]
rs10765657	0.96[CEU][hapmap];0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10765658	0.95[EUR][1000 genomes]
rs10765660	0.94[EUR][1000 genomes]
rs10831173	0.96[EUR][1000 genomes]
rs10831174	0.92[EUR][1000 genomes]
rs10831176	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10831184	0.91[EUR][1000 genomes]
rs11020678	0.97[EUR][1000 genomes]
rs11020679	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11020703	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11020719	0.83[EUR][1000 genomes]
rs12366039	0.94[EUR][1000 genomes]
rs12792677	0.94[EUR][1000 genomes]
rs12808853	0.94[EUR][1000 genomes]
rs1541301	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16920039	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1789652	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1792632	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1857680	0.94[EUR][1000 genomes]
rs1944436	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2000956	0.95[EUR][1000 genomes]
rs2156627	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3020004	0.89[CEU][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs3020016	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes]
rs4597032	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4753131	0.94[EUR][1000 genomes]
rs4753132	0.94[EUR][1000 genomes]
rs480710	0.91[EUR][1000 genomes]
rs581771	0.91[EUR][1000 genomes]
rs613234	0.91[EUR][1000 genomes]
rs655358	0.84[EUR][1000 genomes]
rs689315	0.91[EUR][1000 genomes]
rs7118270	0.91[EUR][1000 genomes]
rs7130456	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7927338	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7927496	0.97[EUR][1000 genomes]
rs7936241	0.94[EUR][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10831169	PANX1	cis	lymphoblastoid	seeQTL
rs10831169	PANX1	cis	parietal	SCAN
rs10831169	RP11-680H20.2	cis	Artery Tibial	GTEx
rs10831169	C11orf54	cis	parietal	SCAN
rs10831169	GPR83	cis	cerebellum	SCAN
rs10831169	GPR83	cis	parietal	SCAN
rs10831169	MRE11A	cis	parietal	SCAN
rs10831169	RP11-680H20.2	cis	Thyroid	GTEx

Chromatin state (count:39 , 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	chr11:93916800-93926200	Weak transcription	HMEC	breast
6	chr11:93917200-93926200	Weak transcription	NHEK	skin
7	chr11:93917600-93923000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:93917600-93925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:93917600-93934200	Weak transcription	Fetal Intestine Small	intestine
10	chr11:93917800-93926400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:93918000-93925600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:93919200-93922200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:93919200-93925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:93919400-93925400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:93919400-93925600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:93919400-93925600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:93919400-93926000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:93919400-93926200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:93919600-93926400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:93920000-93925800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:93920000-93926600	Weak transcription	Fetal Brain Female	brain
22	chr11:93920200-93925600	Weak transcription	NHLF	lung
23	chr11:93920200-93928000	Weak transcription	HSMMtube	muscle
24	chr11:93920400-93924400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:93920400-93925600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:93920400-93925600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:93920400-93925600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:93920400-93925600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:93920400-93925600	Weak transcription	NHDF-Ad	bronchial
30	chr11:93920400-93926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:93920400-93926200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:93920400-93929400	Weak transcription	Pancreas	Pancrea
33	chr11:93920400-93933000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:93920400-93937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:93920600-93925600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:93920600-93926600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:93920600-93927800	Weak transcription	Aorta	Aorta
38	chr11:93921200-93926000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:93922000-93922200	Enhancers	Fetal Intestine Large	intestine

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