Variant report

Variant	rs1147997
Chromosome Location	chr12:75952228-75952229
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10506667	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11180480	0.84[JPT][hapmap]
rs11180560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1147995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11540407	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11610328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11611121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611609	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11830640	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12811160	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12812559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12819511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12822493	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12827986	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1290026	0.98[ASN][1000 genomes]
rs1383100	0.95[ASN][1000 genomes]
rs1501634	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs15513	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1552039	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs17217158	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17220228	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824981	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2054517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2070162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2306391	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2700521	0.98[ASN][1000 genomes]
rs34170388	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35708464	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741495	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3809118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3847669	0.90[YRI][hapmap]
rs3847672	0.98[ASN][1000 genomes]
rs3847673	0.98[ASN][1000 genomes]
rs56049502	0.98[ASN][1000 genomes]
rs56222143	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933387	0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1147997	GLIPR1	cis	normal skin	skin_eQTL
rs1147997	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75944800-75954000	Weak transcription	Pancreas	Pancrea
2	chr12:75946600-75957600	Weak transcription	Fetal Brain Male	brain
3	chr12:75947600-75954000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:75948000-75958200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:75948400-75953800	Weak transcription	HMEC	breast
6	chr12:75948400-75954600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:75948600-75954000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:75948600-75954000	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:75948800-75958200	Weak transcription	Osteobl	bone
10	chr12:75949800-75954800	Enhancers	HepG2	liver
11	chr12:75950600-75953800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:75950600-75954000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:75950600-75954000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:75950800-75954000	Weak transcription	A549	lung
15	chr12:75950800-75959600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:75951400-75954000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:75952000-75952400	Enhancers	Fetal Stomach	stomach
18	chr12:75952000-75952800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:75952000-75953000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:75952000-75954200	Enhancers	Fetal Heart	heart
21	chr12:75952200-75952400	Enhancers	Right Atrium	heart
22	chr12:75952200-75952600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr12:75952200-75952800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:75952200-75952800	Enhancers	Ovary	ovary
25	chr12:75952200-75952800	Enhancers	HSMMtube	muscle
26	chr12:75952200-75953200	Enhancers	Fetal Lung	lung
27	chr12:75952200-75953400	Enhancers	Fetal Kidney	kidney

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