Variant report

Variant	rs15513
Chromosome Location	chr12:75888251-75888252
allele	C/T
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	POLR2A	chr12:75882307-75888804	K562	blood:	n/a	n/a
2	POLR2A	chr12:75888228-75889021	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:75885776..75888514-chr12:75903774..75905483,2	K562	blood:
2	chr12:75884895..75888339-chr12:75903180..75905524,3	MCF-7	breast:
3	chr12:75877168..75879859-chr12:75887104..75889519,2	K562	blood:

Variant related genes	Relation type
ENSG00000257497	TF binding region
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10506667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180480	0.83[JPT][hapmap]
rs11180552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180560	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11355	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609405	0.80[ASN][1000 genomes]
rs11610328	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611121	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11611609	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612665	0.83[ASN][1000 genomes]
rs12425122	0.84[ASN][1000 genomes]
rs12811160	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12812559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815116	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822366	0.83[ASN][1000 genomes]
rs12822493	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12822505	0.83[ASN][1000 genomes]
rs12826635	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827668	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827986	0.81[ASN][1000 genomes]
rs1501634	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552039	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604381	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17218895	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818307	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824981	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2054517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2070162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202105	0.83[ASN][1000 genomes]
rs2279244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306391	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34508642	0.83[ASN][1000 genomes]
rs35124104	0.84[ASN][1000 genomes]
rs35244242	0.83[ASN][1000 genomes]
rs35351465	0.83[ASN][1000 genomes]
rs35619460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741495	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809118	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809121	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420306	0.83[ASN][1000 genomes]
rs4760596	0.83[ASN][1000 genomes]
rs56049502	0.81[ASN][1000 genomes]
rs61933361	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61933362	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933387	0.81[ASN][1000 genomes]
rs7961005	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs15513	GLIPR1	cis	parietal	SCAN
rs15513	KRR1	cis	cerebellum	SCAN
rs15513	GLIPR1	cis	uninvolved skin	skin_eQTL
rs15513	GLIPR1	cis	lesional skin	skin_eQTL
rs15513	LRRN1	trans	cerebellum	SCAN
rs15513	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs15513	GLIPR1	cis	normal skin	skin_eQTL
rs15513	KRR1	cis	parietal	SCAN
rs15513	GLIPR1L2	cis	cerebellum	SCAN
rs15513	GLIPR1L2	cis	parietal	SCAN
rs15513	PTPRB	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75874800-75895000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:75875600-75890200	Weak transcription	Brain Substantia Nigra	brain
3	chr12:75875600-75903400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:75875800-75888800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:75875800-75892400	Weak transcription	K562	blood
6	chr12:75875800-75892600	Weak transcription	Brain Angular Gyrus	brain
7	chr12:75875800-75894400	Weak transcription	Colonic Mucosa	Colon
8	chr12:75875800-75903000	Weak transcription	Small Intestine	intestine
9	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
10	chr12:75876200-75903400	Weak transcription	Fetal Stomach	stomach
11	chr12:75876400-75889800	Weak transcription	Lung	lung
12	chr12:75876400-75891400	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:75876400-75894400	Weak transcription	Ovary	ovary
14	chr12:75876800-75889800	Weak transcription	Left Ventricle	heart
15	chr12:75876800-75889800	Weak transcription	Thymus	Thymus
16	chr12:75876800-75890400	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:75876800-75895000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:75877600-75889000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:75877800-75889000	Weak transcription	Adipose Nuclei	Adipose
20	chr12:75877800-75889200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:75877800-75890200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:75878400-75890600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:75879000-75890000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:75879000-75890800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:75879200-75888600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:75879200-75888800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:75879200-75890600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:75879200-75892400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:75879200-75894400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:75879200-75900600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:75879800-75902000	Strong transcription	Primary B cells from cord blood	blood
32	chr12:75880000-75889000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:75880600-75903800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:75881000-75889000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:75881400-75892600	Weak transcription	Fetal Brain Female	brain
36	chr12:75881400-75894400	Weak transcription	Fetal Kidney	kidney
37	chr12:75881600-75890200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:75882600-75903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:75882800-75890600	Weak transcription	Placenta	Placenta
40	chr12:75883200-75901800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr12:75883400-75894800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:75883400-75902600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr12:75883600-75891600	Weak transcription	Hela-S3	cervix
44	chr12:75883600-75901800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:75883600-75902200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:75883800-75889200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:75883800-75890000	Weak transcription	Psoas Muscle	Psoas
48	chr12:75883800-75890000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr12:75883800-75890000	Weak transcription	HSMMtube	muscle
50	chr12:75883800-75895000	Weak transcription	Right Ventricle	heart

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