Variant report

Variant	rs4393363
Chromosome Location	chr12:75785468-75785469
allele	A/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	EBF1	chr12:75784813-75785495	GM12878	blood:	n/a	n/a
2	RAD21	chr12:75784013-75785591	SK-N-SH	brain:	n/a	n/a
3	MAX	chr12:75784674-75785516	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr12:75785340-75785490	NHDF-neo	bronchial:	n/a	n/a
5	MAX	chr12:75784684-75785494	A549	lung:	n/a	n/a
6	POLR2A	chr12:75784083-75785745	GM12891	blood:	n/a	n/a
7	TCF12	chr12:75784342-75785540	A549	lung:	n/a	n/a
8	MYC	chr12:75784440-75785766	MCF10A-Er-Src	breast:	n/a	chr12:75784525-75784534 chr12:75784526-75784535
9	POLR2A	chr12:75784473-75785512	GM12878	blood:	n/a	n/a
10	CTCF	chr12:75783633-75786193	A549	lung:	n/a	n/a
11	MAX	chr12:75784462-75785486	MCF-7	breast:	n/a	chr12:75784525-75784534 chr12:75784526-75784535
12	POLR2A	chr12:75784683-75785474	H1-hESC	embryonic stem cell:	n/a	n/a
13	GTF2F1	chr12:75784443-75785471	Hela-S3	cervix:	n/a	n/a
14	CREB1	chr12:75784476-75785565	GM12878	blood:	n/a	n/a
15	FOXA2	chr12:75784590-75785504	A549	lung:	n/a	n/a
16	RUNX3	chr12:75784559-75785479	GM12878	blood:	n/a	n/a
17	MXI1	chr12:75784599-75785644	GM12878	blood:	n/a	n/a
18	CTCF	chr12:75784185-75785629	SK-N-SH	brain:	n/a	n/a
19	MAX	chr12:75784558-75785541	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr12:75784306-75785664	MCF10A-Er-Src	breast:	n/a	n/a
21	SMC3	chr12:75784313-75785894	SK-N-SH	brain:	n/a	n/a
22	PML	chr12:75784290-75785498	GM12878	blood:	n/a	chr12:75784524-75784533 chr12:75784527-75784536
23	POLR2A	chr12:75784458-75785494	MCF10A-Er-Src	breast:	n/a	n/a
24	GABPA	chr12:75784533-75785484	MCF-7	breast:	n/a	chr12:75784860-75784874 chr12:75784862-75784871 chr12:75784860-75784871
25	MAX	chr12:75784689-75785483	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr12:75784474-75785608	A549	lung:	n/a	chr12:75784525-75784534 chr12:75784526-75784535
27	NRF1	chr12:75784320-75785577	SK-N-SH	brain:	n/a	chr12:75784860-75784874 chr12:75784862-75784871 chr12:75784860-75784871 chr12:75784860-75784871
28	E2F6	chr12:75784720-75785568	A549	lung:	n/a	chr12:75784861-75784870
29	CTCF	chr12:75785320-75785470	GM12872	blood:	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
CAPS2	TF binding region
ENSG00000139289	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10450780	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10879908	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879909	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879910	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10879912	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10879917	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11180481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180491	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11180502	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11180503	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12366783	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12369849	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12830818	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12833151	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1875468	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2036387	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2173919	0.81[ASN][1000 genomes]
rs3952732	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4019365	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4391857	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479027	0.87[ASN][1000 genomes]
rs4565938	0.85[ASN][1000 genomes]
rs4882599	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4882621	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4882622	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582290	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7135340	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7294749	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7295336	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7296471	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7300308	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310735	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7966751	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4393363	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs4393363	GLIPR1L2	cis	Nerve Tibial	GTEx
rs4393363	GLIPR1L2	cis	Thyroid	GTEx
rs4393363	GLIPR1L2	cis	lung	GTEx
rs4393363	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs4393363	RP11-585P4.5	cis	Artery Tibial	GTEx
rs4393363	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs4393363	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs4393363	GLIPR1L2	cis	Artery Aorta	GTEx
rs4393363	GLIPR1L2	cis	Artery Tibial	GTEx
rs4393363	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs4393363	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs4393363	GLIPR1L2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75782600-75785600	Active TSS	Aorta	Aorta
2	chr12:75782800-75786200	Active TSS	Rectal Smooth Muscle	rectum
3	chr12:75783000-75785800	Active TSS	Right Atrium	heart
4	chr12:75783200-75785800	Active TSS	Colonic Mucosa	Colon
5	chr12:75783400-75785600	Active TSS	Brain Cingulate Gyrus	brain
6	chr12:75783400-75785600	Active TSS	Ovary	ovary
7	chr12:75783400-75785600	Active TSS	Psoas Muscle	Psoas
8	chr12:75783400-75785600	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr12:75783400-75785600	Active TSS	Stomach Smooth Muscle	stomach
10	chr12:75783400-75785800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:75783400-75785800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr12:75783600-75785600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:75783600-75785600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:75783600-75785600	Active TSS	Fetal Lung	lung
15	chr12:75783600-75785600	Active TSS	HSMM	muscle
16	chr12:75783600-75785600	Active TSS	HSMMtube	muscle
17	chr12:75783600-75785800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:75783600-75785800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:75783600-75785800	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr12:75783800-75785600	Active TSS	Brain Substantia Nigra	brain
21	chr12:75784000-75785600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:75784000-75785600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr12:75784000-75785600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:75784000-75785600	Active TSS	Brain Anterior Caudate	brain
25	chr12:75784000-75785600	Active TSS	Fetal Kidney	kidney
26	chr12:75784000-75785600	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr12:75784000-75785800	Active TSS	Brain Angular Gyrus	brain
28	chr12:75784000-75786000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr12:75784200-75785600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:75784200-75785600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:75784200-75785600	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr12:75784200-75785600	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:75784200-75785600	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr12:75784200-75785600	Active TSS	Muscle Satellite Cultured Cells	--
35	chr12:75784200-75785600	Active TSS	Brain Germinal Matrix	brain
36	chr12:75784200-75785600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr12:75784200-75785600	Active TSS	Fetal Brain Female	brain
38	chr12:75784200-75785600	Active TSS	Fetal Intestine Small	intestine
39	chr12:75784200-75785600	Active TSS	Fetal Stomach	stomach
40	chr12:75784200-75785600	Active TSS	NHDF-Ad	bronchial
41	chr12:75784200-75785800	Active TSS	Brain Hippocampus Middle	brain
42	chr12:75784200-75785800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:75784200-75785800	Active TSS	Right Ventricle	heart
44	chr12:75784400-75785600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr12:75784400-75785600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr12:75784400-75785600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:75784400-75785600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:75784400-75785600	Active TSS	Colon Smooth Muscle	Colon
49	chr12:75784400-75785600	Active TSS	Duodenum Mucosa	Duodenum
50	chr12:75784400-75785600	Active TSS	Duodenum Smooth Muscle	Duodenum

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