Variant report

Variant	rs2173919
Chromosome Location	chr12:75869497-75869498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10450780	0.90[ASN][1000 genomes]
rs10879908	0.84[ASN][1000 genomes]
rs10879909	0.84[ASN][1000 genomes]
rs10879910	0.88[ASN][1000 genomes]
rs10879912	0.88[ASN][1000 genomes]
rs10879917	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11180481	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs11180491	0.84[ASN][1000 genomes]
rs11180502	0.83[ASN][1000 genomes]
rs11180503	0.86[ASN][1000 genomes]
rs12366783	0.80[ASN][1000 genomes]
rs12369849	0.84[ASN][1000 genomes]
rs1275478	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1275480	0.87[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs1275481	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs12830818	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1480004	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1604382	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1679378	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697750	0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697752	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697754	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1697756	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1697757	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1795744	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1824980	0.87[EUR][1000 genomes]
rs1875468	0.93[ASN][1000 genomes]
rs2036387	0.92[ASN][1000 genomes]
rs2704766	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2704767	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3952732	0.88[ASN][1000 genomes]
rs4019365	0.92[ASN][1000 genomes]
rs4391857	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4393363	0.81[ASN][1000 genomes]
rs4479027	0.91[ASN][1000 genomes]
rs4565938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882621	0.84[ASN][1000 genomes]
rs4882622	0.83[ASN][1000 genomes]
rs6582290	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7135340	0.84[ASN][1000 genomes]
rs7294749	0.92[ASN][1000 genomes]
rs7296471	0.89[ASN][1000 genomes]
rs7300308	0.89[ASN][1000 genomes]
rs7310735	0.81[ASN][1000 genomes]
rs7966751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971504	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[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
rs2173919	GLIPR1L2	cis	Nerve Tibial	GTEx
rs2173919	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs2173919	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2173919	GLIPR1L2	cis	Artery Tibial	GTEx
rs2173919	GLIPR1L2	cis	Thyroid	GTEx
rs2173919	RP11-585P4.5	cis	Artery Tibial	GTEx
rs2173919	GLIPR1L2	cis	lung	GTEx
rs2173919	GLIPR1	cis	normal skin	skin_eQTL
rs2173919	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs2173919	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs2173919	RP11-585P4.5	cis	Muscle Skeletal	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75865400-75874800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:75866600-75871800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:75866600-75873400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:75867000-75870600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:75868000-75870000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:75868000-75870800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr12:75868200-75871000	Weak transcription	Primary B cells from cord blood	blood
8	chr12:75868400-75874400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:75868400-75875600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:75868600-75873000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:75868600-75874000	Weak transcription	NHEK	skin
12	chr12:75868600-75874600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:75868800-75869800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:75868800-75869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:75868800-75870000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:75868800-75870000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:75868800-75872000	Weak transcription	HMEC	breast
18	chr12:75868800-75873000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:75869000-75870400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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