Variant report

Variant	rs11611121
Chromosome Location	chr12:75877304-75877305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75871827..75875273-chr12:75876446..75879780,3	K562	blood:
2	chr12:75877168..75879859-chr12:75887104..75889519,2	K562	blood:
3	chr12:75873773..75875843-chr12:75876360..75879179,2	K562	blood:
4	chr12:75875820..75878150-chr12:75882711..75885468,3	K562	blood:

Variant related genes	Relation type
ENSG00000139278	Chromatin interaction
ENSG00000257497	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10506667	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10506669	0.86[ASN][1000 genomes]
rs11180480	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs11180499	0.86[ASN][1000 genomes]
rs11180552	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11180560	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11355	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.89[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11609405	0.88[ASN][1000 genomes]
rs11609538	0.83[ASN][1000 genomes]
rs11610328	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11610755	0.80[ASN][1000 genomes]
rs11611609	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11612665	0.91[ASN][1000 genomes]
rs11614719	0.80[ASN][1000 genomes]
rs11616068	0.80[ASN][1000 genomes]
rs11829445	0.80[ASN][1000 genomes]
rs11829975	0.86[ASN][1000 genomes]
rs12423320	0.80[ASN][1000 genomes]
rs12423560	0.86[ASN][1000 genomes]
rs12423750	0.86[ASN][1000 genomes]
rs12424262	0.83[ASN][1000 genomes]
rs12424458	0.80[ASN][1000 genomes]
rs12424779	0.80[ASN][1000 genomes]
rs12425122	0.93[ASN][1000 genomes]
rs12580524	0.86[ASN][1000 genomes]
rs12810889	0.80[ASN][1000 genomes]
rs12811343	0.80[ASN][1000 genomes]
rs12812559	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12813336	0.80[ASN][1000 genomes]
rs12814435	0.80[ASN][1000 genomes]
rs12815116	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12817746	0.86[ASN][1000 genomes]
rs12818326	0.80[ASN][1000 genomes]
rs12819511	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]
rs12821144	0.86[ASN][1000 genomes]
rs12822366	0.91[ASN][1000 genomes]
rs12822493	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12822505	0.91[ASN][1000 genomes]
rs12822654	0.80[ASN][1000 genomes]
rs12826635	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12827668	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12833944	0.86[ASN][1000 genomes]
rs1501634	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs15513	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]
rs1552039	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1604381	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17217158	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17218895	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17818307	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1824981	0.83[EUR][1000 genomes]
rs1909977	0.83[ASN][1000 genomes]
rs2054517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070162	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2134140	0.83[ASN][1000 genomes]
rs2202105	0.91[ASN][1000 genomes]
rs2279244	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306391	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34508642	0.91[ASN][1000 genomes]
rs34522427	0.80[ASN][1000 genomes]
rs34722118	0.80[ASN][1000 genomes]
rs35124104	0.93[ASN][1000 genomes]
rs35244242	0.91[ASN][1000 genomes]
rs35351465	0.91[ASN][1000 genomes]
rs35505142	0.80[ASN][1000 genomes]
rs35619460	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35968211	0.80[ASN][1000 genomes]
rs35986906	0.80[ASN][1000 genomes]
rs36113316	0.86[ASN][1000 genomes]
rs3741495	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809121	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4019356	0.86[ASN][1000 genomes]
rs4420306	0.91[ASN][1000 genomes]
rs4760596	0.91[ASN][1000 genomes]
rs4882626	0.86[ASN][1000 genomes]
rs55742134	0.80[ASN][1000 genomes]
rs55783970	0.80[ASN][1000 genomes]
rs61932180	0.80[ASN][1000 genomes]
rs61933361	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61933362	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66864793	0.80[ASN][1000 genomes]
rs7489329	0.80[ASN][1000 genomes]
rs7961005	0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11611121	GLIPR1	cis	lesional skin	skin_eQTL
rs11611121	GLIPR1	cis	uninvolved skin	skin_eQTL
rs11611121	GLIPR1	cis	normal skin	skin_eQTL
rs11611121	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75873400-75878800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:75873600-75878200	Active TSS	Aorta	Aorta
3	chr12:75873600-75878200	Flanking Active TSS	Dnd41	blood
4	chr12:75873800-75878200	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr12:75873800-75879000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:75874000-75877600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:75874600-75877600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:75874800-75877600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr12:75874800-75878000	Flanking Active TSS	HUVEC	blood vessel
10	chr12:75874800-75895000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:75875000-75877600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:75875200-75877400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr12:75875200-75877800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr12:75875400-75877600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr12:75875400-75887800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:75875600-75877800	Flanking Active TSS	NHDF-Ad	bronchial
17	chr12:75875600-75880600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:75875600-75882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:75875600-75890200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:75875600-75903400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:75875800-75877400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:75875800-75877600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:75875800-75882800	Weak transcription	NHEK	skin
24	chr12:75875800-75883600	Weak transcription	Esophagus	oesophagus
25	chr12:75875800-75886600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:75875800-75886800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:75875800-75888800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:75875800-75892400	Weak transcription	K562	blood
29	chr12:75875800-75892600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:75875800-75894400	Weak transcription	Colonic Mucosa	Colon
31	chr12:75875800-75903000	Weak transcription	Small Intestine	intestine
32	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
33	chr12:75876000-75877400	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
34	chr12:75876000-75877800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr12:75876000-75878400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:75876000-75878400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:75876000-75880600	Transcr. at gene 5' and 3'	Osteobl	bone
38	chr12:75876200-75877600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:75876200-75878800	Weak transcription	A549	lung
40	chr12:75876200-75885000	Weak transcription	Liver	Liver
41	chr12:75876200-75903400	Weak transcription	Fetal Stomach	stomach
42	chr12:75876400-75877400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:75876400-75877400	Enhancers	HSMMtube	muscle
44	chr12:75876400-75877800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:75876400-75878800	Active TSS	GM12878-XiMat	blood
46	chr12:75876400-75879200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
47	chr12:75876400-75881200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:75876400-75883600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:75876400-75886800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:75876400-75889800	Weak transcription	Lung	lung

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