Variant report

Variant	rs13172044
Chromosome Location	chr5:178365742-178365743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRM6-1	chr5:178365678-178366224	ENSG00000272431.1
2	lnc-GRM6-1	chr5:178365678-178366632	ENSG00000248595
3	lnc-GRM6-1	chr5:178364381-178367686	NONHSAT105563

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10042386	0.92[ASN][1000 genomes]
rs10043786	0.81[AMR][1000 genomes]
rs10070619	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11959507	0.89[AMR][1000 genomes]
rs12516516	1.00[JPT][hapmap]
rs13171869	1.00[JPT][hapmap]
rs13177030	0.92[ASN][1000 genomes]
rs13183468	0.91[AMR][1000 genomes]
rs1496948	1.00[JPT][hapmap]
rs17664029	0.85[MEX][hapmap]
rs1826863	0.88[AMR][1000 genomes]
rs1845939	1.00[JPT][hapmap]
rs34551446	0.92[ASN][1000 genomes]
rs34870025	0.88[ASN][1000 genomes]
rs35123052	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35869073	0.83[AMR][1000 genomes]
rs55666251	1.00[ASN][1000 genomes]
rs55841430	0.83[AMR][1000 genomes]
rs6600996	0.89[AMR][1000 genomes]
rs7735200	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]

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	nsv5156	chr5:178346825-178367067	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13172044	BTNL9	cis	cerebellum	SCAN
rs13172044	B4GALT7	cis	parietal	SCAN
rs13172044	EIF4E1B	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178335800-178367000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr5:178341600-178367000	ZNF genes & repeats	Fetal Brain Female	brain
3	chr5:178343000-178367200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr5:178347800-178366800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
5	chr5:178347800-178367400	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr5:178351400-178367400	ZNF genes & repeats	Brain Anterior Caudate	brain
7	chr5:178352200-178366800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
8	chr5:178352200-178367200	ZNF genes & repeats	Brain Substantia Nigra	brain
9	chr5:178352400-178369200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:178353400-178367400	ZNF genes & repeats	Fetal Muscle Leg	muscle
11	chr5:178353600-178365800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
12	chr5:178353800-178366800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
13	chr5:178353800-178367200	ZNF genes & repeats	Brain Hippocampus Middle	brain
14	chr5:178353800-178374800	ZNF genes & repeats	Liver	Liver
15	chr5:178360600-178366600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr5:178360800-178365800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
17	chr5:178361600-178365800	ZNF genes & repeats	Left Ventricle	heart
18	chr5:178362800-178369000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
19	chr5:178363200-178369000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr5:178363400-178367400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:178363800-178367200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
22	chr5:178363800-178369000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:178364000-178368800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr5:178364600-178369200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr5:178364800-178365800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
26	chr5:178365000-178367200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:178365000-178367200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:178365000-178367400	ZNF genes & repeats	Fetal Lung	lung
29	chr5:178365000-178367600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:178365200-178367400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
31	chr5:178365200-178367400	ZNF genes & repeats	Fetal Stomach	stomach
32	chr5:178365200-178369200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:178365400-178365800	ZNF genes & repeats	Ovary	ovary

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