Variant report

Variant	rs58412666
Chromosome Location	chr11:45378013-45378014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRDM11-3	chr11:45377947-45378165	XLOC_009120
2	lnc-PRDM11-3	chr11:45377947-45378195	XLOC_009120
3	lnc-PRDM11-3	chr11:45377947-45378689	XLOC_009120
4	lnc-PRDM11-3	chr11:45377430-45378199	ENSG00000254427
5	lnc-PRDM11-3	chr11:45377947-45378204	ENSG00000254427
6	lnc-PRDM11-3	chr11:45377249-45378689	NONHSAT019018

Extended variants
information (count: 3 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11038413	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485621	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530619	chr11:45294176-45553928	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58412666	RP11-430H10.1	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45377000-45378200	Enhancers	Small Intestine	intestine
2	chr11:45377200-45378200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr11:45377400-45378200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:45377400-45378200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:45377400-45378200	Flanking Active TSS	Brain Germinal Matrix	brain
6	chr11:45377600-45378200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:45377600-45378200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr11:45377600-45378200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr11:45377600-45378200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:45377600-45378200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr11:45377600-45378200	Flanking Active TSS	Fetal Brain Female	brain
12	chr11:45377600-45378200	Enhancers	Fetal Lung	lung
13	chr11:45377600-45378600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:45377600-45380200	Weak transcription	Aorta	Aorta
15	chr11:45377800-45378200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr11:45377800-45378200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr11:45377800-45378200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr11:45377800-45378200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr11:45377800-45378200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr11:45377800-45378200	Enhancers	Brain Substantia Nigra	brain
21	chr11:45377800-45378200	Enhancers	Fetal Brain Male	brain
22	chr11:45377800-45378200	Enhancers	Fetal Intestine Small	intestine
23	chr11:45377800-45378200	Enhancers	Fetal Stomach	stomach
24	chr11:45377800-45378800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr11:45378000-45378200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
26	chr11:45378000-45378200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:45378000-45378200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:45378000-45378200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr11:45378000-45378200	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr11:45378000-45378200	Enhancers	Primary T cells from cord blood	blood
31	chr11:45378000-45378200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr11:45378000-45378200	Enhancers	Brain Anterior Caudate	brain
33	chr11:45378000-45378200	Enhancers	Brain Cingulate Gyrus	brain
34	chr11:45378000-45378200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr11:45378000-45378200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:45378000-45378200	Enhancers	Fetal Thymus	thymus
37	chr11:45378000-45378400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr11:45378000-45387800	Weak transcription	Lung	lung

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