Variant report

Variant	rs4882689
Chromosome Location	chr12:75761968-75761969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10506668	0.86[JPT][hapmap]
rs10785187	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10879900	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879902	0.88[CHB][hapmap]
rs10879903	0.87[CHB][hapmap]
rs10879905	0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10879906	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10879907	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10879922	0.82[JPT][hapmap]
rs11180455	0.81[JPT][hapmap]
rs11180456	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11180458	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11180460	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs11180465	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11180470	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11180473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180474	0.87[CHB][hapmap]
rs11180475	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11180483	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11180484	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11180488	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11180489	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11180492	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11180512	0.82[JPT][hapmap]
rs11180540	0.82[JPT][hapmap]
rs11180548	0.82[JPT][hapmap]
rs11520223	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11610111	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11610112	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11831200	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs11837697	0.83[AMR][1000 genomes]
rs12366348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12367329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12368429	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12369556	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12369854	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12371293	0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12372516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12581394	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12581416	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs1909979	0.82[JPT][hapmap]
rs3087687	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[AMR][1000 genomes]
rs3923914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4394867	0.86[JPT][hapmap]
rs4409878	0.82[JPT][hapmap]
rs4415811	0.82[JPT][hapmap]
rs4565940	0.86[JPT][hapmap]
rs4583012	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4623941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4882616	0.86[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4882618	0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4882619	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4882620	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4882687	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60971359	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67904412	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7135440	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7136911	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297994	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs7298343	0.81[CEU][hapmap]
rs73191008	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73364090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73364096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73365996	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7954879	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967619	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969930	0.82[JPT][hapmap]
rs7970188	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7970458	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7974011	0.82[JPT][hapmap]
rs7975661	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7978312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7978856	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1054059	chr12:75654631-75776721	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv899312	chr12:75692261-75790817	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	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
6	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
7	esv3407693	chr12:75761816-75762397	Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs4882689	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs4882689	RP11-585P4.5	cis	Thyroid	GTEx
rs4882689	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs4882689	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs4882689	GLIPR1L2	cis	Stomach	GTEx
rs4882689	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs4882689	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs4882689	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs4882689	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs4882689	GLIPR1L1	cis	multi-tissue	Pritchard
rs4882689	GLIPR1L2	cis	Nerve Tibial	GTEx
rs4882689	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs4882689	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs4882689	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs4882689	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs4882689	GLIPR1L2	cis	Artery Aorta	GTEx
rs4882689	GLIPR1L2	cis	Thyroid	GTEx
rs4882689	GLIPR1L2	cis	lung	GTEx
rs4882689	GLIPR1L2	cis	Artery Tibial	GTEx
rs4882689	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs4882689	RP11-585P4.5	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75749600-75782800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:75749800-75771800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:75754000-75784200	Weak transcription	Right Ventricle	heart
4	chr12:75757200-75783400	Weak transcription	Ovary	ovary
5	chr12:75758200-75782600	Weak transcription	Aorta	Aorta
6	chr12:75760400-75763400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:75760800-75762600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:75760800-75763200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:75760800-75766400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:75761000-75762200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:75761000-75763800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:75761600-75763200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr12:75761800-75762000	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr12:75761800-75763800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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