Variant report

Variant	rs12332469
Chromosome Location	chr5:179382594-179382595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D9B-4	chr5:179382480-179382669	NONHSAT105661

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10054440	1.00[ASW][hapmap]
rs10054685	1.00[ASW][hapmap];0.85[LWK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10056758	0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10059710	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10060093	1.00[ASW][hapmap];0.85[LWK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10061208	1.00[ASW][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10076682	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10479552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11949896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11958554	1.00[AMR][1000 genomes]
rs11959514	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73344319	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9329091	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12332469	NFIL3	trans	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179370000-179382800	Weak transcription	Lung	lung
2	chr5:179370200-179392800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:179370800-179386800	Weak transcription	HepG2	liver
4	chr5:179372200-179386800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:179373000-179382800	Weak transcription	Brain Anterior Caudate	brain
6	chr5:179373000-179389600	Weak transcription	Fetal Intestine Large	intestine
7	chr5:179373200-179383000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:179373400-179400600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:179373800-179401600	Weak transcription	Colonic Mucosa	Colon
10	chr5:179374000-179386000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:179374600-179387200	Weak transcription	HSMMtube	muscle
12	chr5:179374600-179387400	Weak transcription	Pancreas	Pancrea
13	chr5:179375000-179382800	Weak transcription	Fetal Stomach	stomach
14	chr5:179375400-179392600	Weak transcription	Fetal Kidney	kidney
15	chr5:179376600-179389800	Weak transcription	Placenta	Placenta
16	chr5:179376600-179390000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:179376600-179406600	Weak transcription	Psoas Muscle	Psoas
18	chr5:179376800-179382600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:179379000-179383000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:179379000-179389800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:179379000-179390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:179379400-179386200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:179379400-179387200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:179380000-179382600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:179380000-179392600	Weak transcription	NH-A	brain
26	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
27	chr5:179380200-179389800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:179380200-179401200	Weak transcription	Esophagus	oesophagus
29	chr5:179380400-179383400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:179380400-179389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:179380400-179393600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:179380800-179383000	Strong transcription	Adipose Nuclei	Adipose
33	chr5:179381000-179383000	Strong transcription	Brain Angular Gyrus	brain
34	chr5:179381000-179383200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:179381000-179383400	Strong transcription	Primary B cells from cord blood	blood
36	chr5:179381000-179383800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:179381000-179383800	Strong transcription	Primary hematopoietic stem cells	blood
38	chr5:179381000-179384000	Strong transcription	Liver	Liver
39	chr5:179381000-179384200	Strong transcription	Brain Hippocampus Middle	brain
40	chr5:179381000-179384600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr5:179381000-179385800	Strong transcription	Brain Substantia Nigra	brain
42	chr5:179381000-179385800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr5:179381000-179389200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:179381000-179397000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr5:179381000-179397200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:179381000-179407800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:179381200-179382600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:179381200-179382600	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr5:179381200-179383800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr5:179381200-179384800	Strong transcription	Fetal Muscle Trunk	muscle

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