Variant report

Variant	rs733881
Chromosome Location	chr12:75976111-75976112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75976057..75978739-chr12:76422916..76424954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10748283	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10748284	0.89[CHB][hapmap]
rs10785195	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785199	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10785200	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10879929	0.81[EUR][1000 genomes]
rs10879930	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10879932	0.80[EUR][1000 genomes]
rs10879933	0.82[EUR][1000 genomes]
rs10879934	0.80[EUR][1000 genomes]
rs10879935	0.81[EUR][1000 genomes]
rs10879936	0.89[CEU][hapmap]
rs10879937	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10879938	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10879943	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10879945	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs10879947	0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs11180575	0.82[EUR][1000 genomes]
rs11180584	0.81[EUR][1000 genomes]
rs11180601	0.84[ASN][1000 genomes]
rs11495681	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12310185	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1466464	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1480005	0.95[EUR][1000 genomes]
rs1697759	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17115238	0.85[CEU][hapmap]
rs2366988	0.89[CEU][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2366989	0.89[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs3847671	0.80[EUR][1000 genomes]
rs3898937	0.81[EUR][1000 genomes]
rs4323912	0.83[EUR][1000 genomes]
rs4882601	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4882602	0.90[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs4882631	0.85[CEU][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs4882639	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4882640	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7137366	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs7300994	0.82[EUR][1000 genomes]
rs7314220	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs733880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955264	0.81[EUR][1000 genomes]
rs7956673	0.80[CEU][hapmap]
rs7956799	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958075	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs7958760	0.90[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs7980645	0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs7980713	0.81[EUR][1000 genomes]
rs899659	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9634253	0.85[CEU][hapmap];0.95[GIH][hapmap]

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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs733881	GLIPR1	cis	parietal	SCAN
rs733881	GLIPR1L2	cis	Nerve Tibial	GTEx
rs733881	GLIPR1L2	cis	parietal	SCAN
rs733881	GLIPR1	cis	cerebellum	SCAN
rs733881	GLIPR1L2	cis	cerebellum	SCAN
rs733881	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs733881	KRR1	cis	cerebellum	SCAN
rs733881	GLIPR1L2	cis	Artery Tibial	GTEx
rs733881	GLIPR1L2	cis	lung	GTEx
rs733881	KRR1	cis	parietal	SCAN
rs733881	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs733881	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs733881	GLIPR1L2	cis	Thyroid	GTEx
rs733881	RP11-585P4.5	cis	Thyroid	GTEx
rs733881	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs733881	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs733881	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs733881	GLIPR1L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75965400-75977200	Weak transcription	Fetal Brain Female	brain
2	chr12:75967000-75978800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:75973600-75978800	Weak transcription	A549	lung
4	chr12:75973600-75979600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:75973800-75976400	Weak transcription	HepG2	liver
6	chr12:75974800-75977600	Enhancers	Fetal Lung	lung
7	chr12:75976000-75978400	Weak transcription	NHDF-Ad	bronchial
8	chr12:75976000-75978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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