Variant report

Variant	rs7315474
Chromosome Location	chr12:76029916-76029917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76028709..76030372-chr12:76096874..76098526,2	MCF-7	breast:
2	chr12:76028267..76031112-chr12:76369417..76371857,2	MCF-7	breast:
3	chr12:76028950..76031256-chr12:76042854..76044405,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10748284	0.83[CEU][hapmap]
rs10785198	0.85[ASN][1000 genomes]
rs10879929	0.82[ASN][1000 genomes]
rs10879932	0.82[ASN][1000 genomes]
rs10879933	0.82[ASN][1000 genomes]
rs10879934	0.83[ASN][1000 genomes]
rs10879935	0.83[ASN][1000 genomes]
rs10879936	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10879945	0.86[GIH][hapmap]
rs10879949	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180575	0.82[ASN][1000 genomes]
rs11180584	0.83[ASN][1000 genomes]
rs11180598	0.93[ASN][1000 genomes]
rs11180603	0.90[ASN][1000 genomes]
rs11514051	0.81[ASN][1000 genomes]
rs11519910	0.85[ASN][1000 genomes]
rs11520226	0.85[ASN][1000 genomes]
rs12811250	0.83[ASN][1000 genomes]
rs17115238	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2054516	0.96[ASN][1000 genomes]
rs2366988	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2366989	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2886828	0.91[ASN][1000 genomes]
rs34406885	0.83[ASN][1000 genomes]
rs3847671	0.82[ASN][1000 genomes]
rs4323912	0.81[ASN][1000 genomes]
rs4882631	0.91[CHB][hapmap];0.80[CHD][hapmap]
rs4882635	0.84[ASN][1000 genomes]
rs58886425	0.92[ASN][1000 genomes]
rs60465677	0.85[ASN][1000 genomes]
rs6582293	0.94[ASN][1000 genomes]
rs6582294	0.99[ASN][1000 genomes]
rs7137610	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7297580	0.96[ASN][1000 genomes]
rs7300994	0.81[ASN][1000 genomes]
rs7305673	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7314159	0.83[ASN][1000 genomes]
rs7314220	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7955264	0.81[ASN][1000 genomes]
rs7956673	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7956953	0.92[ASN][1000 genomes]
rs7958508	0.87[ASN][1000 genomes]
rs7962144	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7962276	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs7979460	0.92[ASN][1000 genomes]
rs7979600	0.85[ASN][1000 genomes]
rs7980713	0.83[ASN][1000 genomes]
rs9634253	0.95[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs7315474	GLIPR1L1	cis	lymphoblastoid	seeQTL
rs7315474	GLIPR1L2	cis	Nerve Tibial	GTEx
rs7315474	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs7315474	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs7315474	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs7315474	GLIPR1	cis	cerebellum	SCAN
rs7315474	GLIPR1L2	cis	Thyroid	GTEx
rs7315474	KRR1	cis	parietal	SCAN
rs7315474	GLIPR1L2	cis	parietal	SCAN
rs7315474	KRR1	cis	cerebellum	SCAN
rs7315474	GLIPR1L2	cis	cerebellum	SCAN
rs7315474	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs7315474	GLIPR1L2	cis	Artery Tibial	GTEx
rs7315474	RP11-585P4.5	cis	Artery Tibial	GTEx
rs7315474	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs7315474	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs7315474	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs7315474	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs7315474	GLIPR1L2	cis	lung	GTEx
rs7315474	RP11-585P4.5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76025400-76030800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr12:76025600-76032400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:76025800-76030200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:76026200-76030200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr12:76026600-76035000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:76027400-76030000	Enhancers	Fetal Lung	lung
7	chr12:76027600-76030200	Enhancers	HUVEC	blood vessel
8	chr12:76027600-76031000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:76027800-76031000	Enhancers	HepG2	liver
10	chr12:76028000-76030600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:76028200-76030000	Enhancers	K562	blood
12	chr12:76028200-76030200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:76028200-76030800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:76028200-76031000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr12:76028400-76030200	Enhancers	HSMM	muscle
16	chr12:76028400-76030400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:76028400-76030600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr12:76028600-76030400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr12:76028600-76030400	Enhancers	NHDF-Ad	bronchial
20	chr12:76028600-76030400	Enhancers	NHLF	lung
21	chr12:76028600-76030400	Enhancers	Osteobl	bone
22	chr12:76028600-76031000	Enhancers	NH-A	brain
23	chr12:76028800-76030400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr12:76028800-76030400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:76028800-76030600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:76028800-76030800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:76028800-76031000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:76028800-76031000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:76029000-76030000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:76029000-76030200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:76029200-76030000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr12:76029200-76031000	Enhancers	HMEC	breast
33	chr12:76029400-76030200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:76029400-76030200	Enhancers	GM12878-XiMat	blood
35	chr12:76029400-76030200	Enhancers	HSMMtube	muscle
36	chr12:76029400-76030400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:76029400-76030400	Enhancers	NHEK	skin
38	chr12:76029400-76030600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:76029400-76034400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:76029600-76030000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:76029600-76030400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:76029600-76033600	Weak transcription	Dnd41	blood
43	chr12:76029800-76030400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:76029800-76030400	Enhancers	A549	lung

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