Variant report

Variant	rs2279244
Chromosome Location	chr12:75896664-75896665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75895029..75896766-chr12:75903293..75906577,3	MCF-7	breast:
2	chr12:75879283..75886841-chr12:75892353..75898321,9	K562	blood:
3	chr12:75895269..75897744-chr12:75903455..75905180,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257497	Chromatin interaction
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 13 )

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];1.00[YRI][hapmap]
rs11180480	0.83[JPT][hapmap]
rs11180552	0.96[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.91[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609405	0.80[ASN][1000 genomes]
rs11610328	0.80[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611121	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]
rs11611609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815116	1.00[AFR][1000 genomes];0.97[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];0.96[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	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827668	0.92[AFR][1000 genomes];1.00[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15513	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]
rs1552039	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604381	0.97[AFR][1000 genomes];0.97[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];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17218895	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818307	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824981	0.82[AMR][1000 genomes];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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202105	0.83[ASN][1000 genomes]
rs2306391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[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	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741495	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809121	0.93[AFR][1000 genomes];0.97[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61933362	1.00[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2279244	GLIPR1	cis	parietal	SCAN
rs2279244	GLIPR1L2	cis	parietal	SCAN
rs2279244	GLIPR1	cis	normal skin	skin_eQTL
rs2279244	GLIPR1	cis	lymphoblastoid	seeQTL
rs2279244	PTPRB	cis	parietal	SCAN
rs2279244	KRR1	cis	parietal	SCAN
rs2279244	GLIPR1L2	cis	cerebellum	SCAN
rs2279244	GLIPR1	cis	lesional skin	skin_eQTL
rs2279244	KRR1	cis	cerebellum	SCAN
rs2279244	KRR1	cis	Muscle Skeletal	GTEx
rs2279244	GLIPR1	cis	uninvolved skin	skin_eQTL
rs2279244	LRRN1	trans	cerebellum	SCAN
rs2279244	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75875600-75903400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:75875800-75903000	Weak transcription	Small Intestine	intestine
3	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
4	chr12:75876200-75903400	Weak transcription	Fetal Stomach	stomach
5	chr12:75879200-75900600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:75879800-75902000	Strong transcription	Primary B cells from cord blood	blood
7	chr12:75880600-75903800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:75882600-75903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:75883200-75901800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:75883400-75902600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr12:75883600-75901800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:75883600-75902200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr12:75883800-75904800	Weak transcription	Esophagus	oesophagus
14	chr12:75884000-75899400	Strong transcription	HSMM	muscle
15	chr12:75884200-75899000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:75884200-75901200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:75884200-75901200	Strong transcription	NH-A	brain
18	chr12:75884200-75902200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:75884400-75901600	Strong transcription	NHDF-Ad	bronchial
20	chr12:75884800-75899200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:75885000-75902200	Strong transcription	HUVEC	blood vessel
22	chr12:75885000-75902400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:75886200-75903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:75886400-75899400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:75886600-75901400	Strong transcription	HMEC	breast
26	chr12:75886600-75903000	Strong transcription	Fetal Thymus	thymus
27	chr12:75886800-75902000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:75887000-75899200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr12:75887000-75900600	Strong transcription	A549	lung
30	chr12:75887000-75902200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:75887200-75901000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:75887200-75902200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:75887400-75898600	Strong transcription	Osteobl	bone
34	chr12:75887400-75901800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:75887400-75903000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:75887600-75900400	Strong transcription	Primary hematopoietic stem cells	blood
37	chr12:75887600-75901200	Strong transcription	Dnd41	blood
38	chr12:75887600-75901800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:75887600-75902000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:75887600-75902000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr12:75887600-75902400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:75887800-75902600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:75888000-75903000	Weak transcription	Pancreas	Pancrea
44	chr12:75888200-75898400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:75888600-75900800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:75888600-75901800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:75888600-75903200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:75888800-75902200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:75888800-75903800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:75888800-75904200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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