Variant report

Variant	rs4391857
Chromosome Location	chr12:75783542-75783543
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr12:75782792-75783918	MCF10A-Er-Src	breast:	n/a	chr12:75783015-75783026
2	TCF12	chr12:75782560-75783646	SK-N-SH	brain:	n/a	n/a
3	TEAD4	chr12:75782668-75783560	SK-N-SH	brain:	n/a	n/a
4	EP300	chr12:75782667-75783550	SK-N-SH	brain:	n/a	chr12:75782752-75782761 chr12:75783503-75783517
5	SP1	chr12:75782541-75783817	HCT-116	colon:	n/a	n/a
6	POLR2A	chr12:75783463-75783612	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr12:75783249-75783621	MCF10A-Er-Src	breast:	n/a	n/a
8	EP300	chr12:75782535-75784131	SK-N-SH	brain:	n/a	chr12:75782752-75782761 chr12:75783503-75783517 chr12:75784067-75784081
9	JUND	chr12:75782181-75783826	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr12:75782547-75783579	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr12:75782679-75783544	SK-N-SH	brain:	n/a	n/a
12	E2F4	chr12:75783004-75783691	MCF10A-Er-Src	breast:	n/a	n/a
13	JUND	chr12:75782508-75783557	HCT-116	colon:	n/a	n/a
14	POLR2A	chr12:75782886-75783542	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75783435..75786287-chr12:76426934..76428474,2	MCF-7	breast:

Variant related genes	Relation type
GLIPR1L2	TF binding region
ENSG00000139289	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10450780	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10879908	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879909	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879910	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10879912	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10879917	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11180481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180491	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11180502	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11180503	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12366783	0.93[ASN][1000 genomes]
rs12369849	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1275478	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1275480	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs1275481	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12830818	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12833151	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1604382	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1697750	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs1697752	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1697754	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1875468	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2036387	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2173919	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2704766	0.85[JPT][hapmap]
rs2704767	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3952732	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4019365	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4393363	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479027	0.87[ASN][1000 genomes]
rs4565938	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4882599	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4882621	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4882622	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582290	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7135340	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7294749	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7295336	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7296471	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7300308	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310735	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7966751	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][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	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	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
4	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
5	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription 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	27 gene(s)	inside rSNPs	diseases
8	esv3374621	chr12:75783234-75806310	Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4391857	GLIPR1L2	cis	Artery Aorta	GTEx
rs4391857	GLIPR1L2	cis	Nerve Tibial	GTEx
rs4391857	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs4391857	GLIPR1L2	cis	Thyroid	GTEx
rs4391857	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs4391857	GLIPR1	cis	normal skin	skin_eQTL
rs4391857	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs4391857	RP11-585P4.5	cis	Artery Tibial	GTEx
rs4391857	GLIPR1L2	cis	Artery Tibial	GTEx
rs4391857	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs4391857	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs4391857	GLIPR1L2	cis	lung	GTEx
rs4391857	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs4391857	GLIPR1L2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75754000-75784200	Weak transcription	Right Ventricle	heart
2	chr12:75763400-75784400	Weak transcription	Left Ventricle	heart
3	chr12:75772200-75785000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:75776600-75784800	Weak transcription	Gastric	stomach
5	chr12:75782200-75784200	Enhancers	Hela-S3	cervix
6	chr12:75782400-75783600	Enhancers	Brain Anterior Caudate	brain
7	chr12:75782400-75783800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:75782400-75784000	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:75782400-75784200	Enhancers	HUVEC	blood vessel
10	chr12:75782400-75784400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:75782600-75783600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:75782600-75784000	Enhancers	NH-A	brain
13	chr12:75782600-75784200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:75782600-75784200	Enhancers	NHEK	skin
15	chr12:75782600-75784600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:75782600-75784800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:75782600-75785600	Active TSS	Aorta	Aorta
18	chr12:75782800-75783600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:75782800-75783600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:75782800-75783800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:75782800-75783800	Flanking Active TSS	GM12878-XiMat	blood
22	chr12:75782800-75784000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr12:75782800-75784200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr12:75782800-75784400	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:75782800-75784600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:75782800-75786200	Active TSS	Rectal Smooth Muscle	rectum
27	chr12:75783000-75783600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr12:75783000-75783600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr12:75783000-75783600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:75783000-75783600	Enhancers	Brain Substantia Nigra	brain
31	chr12:75783000-75783600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr12:75783000-75783600	Enhancers	HSMMtube	muscle
33	chr12:75783000-75784000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:75783000-75784200	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr12:75783000-75784400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:75783000-75784400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr12:75783000-75784600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr12:75783000-75784600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:75783000-75784600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:75783000-75785800	Active TSS	Right Atrium	heart
41	chr12:75783200-75783600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr12:75783200-75783600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:75783200-75783600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:75783200-75783600	Active TSS	Brain Angular Gyrus	brain
45	chr12:75783200-75783600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr12:75783200-75784000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr12:75783200-75784000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr12:75783200-75784000	Weak transcription	Small Intestine	intestine
49	chr12:75783200-75784000	Active TSS	NHLF	lung
50	chr12:75783200-75784200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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