Variant report

Variant	rs7300994
Chromosome Location	chr12:75957821-75957822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75955678..75958303-chr12:75962611..75964917,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10748282	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10785195	0.82[EUR][1000 genomes]
rs10785198	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10879929	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10879930	0.82[EUR][1000 genomes]
rs10879932	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10879933	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10879934	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10879935	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10879936	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180562	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11180575	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11180584	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180598	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11180603	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11514051	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11519910	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11520226	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12811250	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1697759	0.82[EUR][1000 genomes]
rs17115238	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054518	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2366988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366989	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2886826	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34406885	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3847671	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3898937	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4323912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882631	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882635	0.80[ASN][1000 genomes]
rs58886425	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60465677	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6582293	0.86[EUR][1000 genomes]
rs7137610	0.85[EUR][1000 genomes]
rs7305673	0.86[EUR][1000 genomes]
rs7314220	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315474	0.81[ASN][1000 genomes]
rs733880	0.82[EUR][1000 genomes]
rs733881	0.82[EUR][1000 genomes]
rs7955264	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956673	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7956799	0.81[EUR][1000 genomes]
rs7956953	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7958508	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7962144	0.84[EUR][1000 genomes]
rs7962276	0.86[EUR][1000 genomes]
rs7979460	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979600	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7980713	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9634253	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	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
6	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7300994	GLIPR1L2	cis	Nerve Tibial	GTEx
rs7300994	GLIPR1L2	cis	lung	GTEx
rs7300994	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs7300994	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs7300994	GLIPR1L2	cis	Artery Tibial	GTEx
rs7300994	GLIPR1L2	cis	Thyroid	GTEx
rs7300994	RP11-585P4.5	cis	Artery Tibial	GTEx
rs7300994	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs7300994	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs7300994	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs7300994	GLIPR1L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75948000-75958200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:75948800-75958200	Weak transcription	Osteobl	bone
3	chr12:75950800-75959600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:75953800-75959000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:75954600-75964800	Weak transcription	Brain Substantia Nigra	brain
6	chr12:75954800-75958200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:75954800-75958200	Weak transcription	HMEC	breast
8	chr12:75955000-75958200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:75955800-75958200	Weak transcription	Spleen	Spleen
10	chr12:75956400-75961400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:75956600-75958200	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:75957000-75959000	Enhancers	HUVEC	blood vessel
13	chr12:75957200-75958800	Enhancers	Fetal Brain Female	brain
14	chr12:75957200-75959000	Enhancers	NHDF-Ad	bronchial
15	chr12:75957200-75960200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:75957400-75958200	Weak transcription	Esophagus	oesophagus
17	chr12:75957400-75958400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:75957600-75958400	Enhancers	Fetal Muscle Trunk	muscle
19	chr12:75957600-75958800	Enhancers	Fetal Brain Male	brain
20	chr12:75957800-75958600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:75957800-75959000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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