Variant report

Variant	rs3847669
Chromosome Location	chr12:75949158-75949159
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75948608..75951291-chr12:76423919..76425941,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139289	Chromatin interaction
ENSG00000257453	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10879928	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1147994	0.83[CEU][hapmap]
rs1147995	0.90[YRI][hapmap]
rs1148003	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148004	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1275474	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1275481	0.82[CHD][hapmap]
rs1679381	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795379	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1824980	0.87[ASN][1000 genomes]
rs1824982	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2366987	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3858534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3847669	GLIPR1L2	cis	cerebellum	SCAN
rs3847669	GLIPR1L2	cis	parietal	SCAN
rs3847669	GLIPR1	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr12:75947600-75949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:75947600-75954000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:75947800-75952200	Weak transcription	Fetal Kidney	kidney
6	chr12:75948000-75950000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:75948000-75952000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:75948000-75958200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:75948200-75952000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:75948400-75949800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:75948400-75949800	Weak transcription	Fetal Lung	lung
12	chr12:75948400-75949800	Weak transcription	A549	lung
13	chr12:75948400-75950000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:75948400-75950200	Weak transcription	Fetal Stomach	stomach
15	chr12:75948400-75952000	Weak transcription	Right Atrium	heart
16	chr12:75948400-75952200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:75948400-75953800	Weak transcription	HMEC	breast
18	chr12:75948400-75954600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:75948600-75949800	Weak transcription	HepG2	liver
20	chr12:75948600-75950000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:75948600-75952200	Weak transcription	HSMMtube	muscle
22	chr12:75948600-75954000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:75948600-75954000	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:75948800-75949800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:75948800-75950200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:75948800-75952000	Weak transcription	Fetal Heart	heart
27	chr12:75948800-75958200	Weak transcription	Osteobl	bone
28	chr12:75949000-75950200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:75949000-75950200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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