Variant report

Variant	rs4472973
Chromosome Location	chr12:75727645-75727646
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10879901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11180469	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11180553	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs12579473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12828263	1.00[YRI][hapmap]
rs28578562	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv520424	chr12:75646788-75740883	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv526556	chr12:75653281-75740883	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1054059	chr12:75654631-75776721	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv899312	chr12:75692261-75790817	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4472973	GLIPR1L2	cis	Artery Tibial	GTEx
rs4472973	GLIPR1L2	cis	cerebellum	SCAN
rs4472973	GLIPR1L2	cis	parietal	SCAN
rs4472973	GLIPR1L2	cis	Muscle Skeletal	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75724000-75728000	Weak transcription	Stomach Mucosa	stomach
2	chr12:75724000-75728000	Weak transcription	Spleen	Spleen
3	chr12:75724000-75728400	Weak transcription	Fetal Heart	heart
4	chr12:75724200-75728000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:75724200-75728000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:75724200-75728000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:75724200-75728000	Weak transcription	Placenta	Placenta
8	chr12:75724200-75728000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:75724200-75728000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:75724200-75728200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:75724200-75728200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:75724200-75728200	Weak transcription	Lung	lung
13	chr12:75724200-75728200	Weak transcription	Pancreas	Pancrea
14	chr12:75724200-75728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:75724200-75728400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:75724200-75728400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:75724400-75727800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:75724400-75727800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:75724400-75727800	Weak transcription	Brain Substantia Nigra	brain
20	chr12:75724400-75728000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:75724400-75728000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:75724400-75728000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr12:75724400-75728000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr12:75724400-75728000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:75724400-75728000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:75724400-75728000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:75724400-75728000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:75724400-75728000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:75724400-75728000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:75724400-75728000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:75724400-75728000	Weak transcription	Brain Angular Gyrus	brain
32	chr12:75724400-75728000	Weak transcription	Brain Germinal Matrix	brain
33	chr12:75724400-75728000	Weak transcription	Fetal Kidney	kidney
34	chr12:75724400-75728000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr12:75724400-75728000	Weak transcription	Fetal Thymus	thymus
36	chr12:75724400-75728000	Weak transcription	Right Atrium	heart
37	chr12:75724400-75728000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:75724400-75728000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr12:75724400-75728000	Weak transcription	HMEC	breast
40	chr12:75724400-75728000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr12:75724400-75728000	Weak transcription	NH-A	brain
42	chr12:75724400-75728000	Weak transcription	NHDF-Ad	bronchial
43	chr12:75724400-75728000	Weak transcription	Osteobl	bone
44	chr12:75724400-75728200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:75724400-75728200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:75724400-75728200	Weak transcription	HUVEC	blood vessel
47	chr12:75724400-75728400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:75724400-75728400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:75724400-75728400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:75724400-75728400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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