Variant report

Variant	rs7975661
Chromosome Location	chr12:75696430-75696431
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	chr12:75694427..75696955-chr12:75721959..75724062,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180881	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10506668	0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs1051446	0.85[MEX][hapmap];0.90[TSI][hapmap]
rs10785187	0.81[JPT][hapmap]
rs10879900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879902	0.87[CHB][hapmap]
rs10879903	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs10879905	0.82[JPT][hapmap]
rs10879922	1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11180441	0.82[JPT][hapmap]
rs11180455	0.82[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs11180456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11180458	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180460	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs11180465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11180470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs11180473	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11180474	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs11180475	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11180483	0.82[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs11180512	0.81[JPT][hapmap]
rs11180540	0.95[MEX][hapmap];0.88[TSI][hapmap]
rs11180548	1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11520223	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11610111	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11610112	0.81[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11831200	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11837697	0.80[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes]
rs12366348	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12367329	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12368429	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12369556	0.82[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs12369854	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12371293	0.82[JPT][hapmap]
rs12372516	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12581394	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12581416	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs17115098	0.81[JPT][hapmap]
rs1909979	0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2242435	0.90[MEX][hapmap]
rs3087687	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs3741496	0.85[MEX][hapmap];0.88[TSI][hapmap]
rs4394867	0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4409878	0.81[JPT][hapmap]
rs4415811	0.82[JPT][hapmap]
rs4565940	0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4623941	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4882616	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes]
rs4882618	0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs4882687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4882689	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]
rs60971359	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap]
rs7298343	0.85[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs73364090	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73364096	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7485576	0.81[CHD][hapmap]
rs7954879	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967619	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969930	0.95[MEX][hapmap];0.85[TSI][hapmap]
rs7970188	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7974011	0.95[MEX][hapmap];0.87[TSI][hapmap]
rs7978312	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv520424	chr12:75646788-75740883	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv526556	chr12:75653281-75740883	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	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
6	nsv899309	chr12:75664655-75712662	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv899310	chr12:75682796-75707396	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv899311	chr12:75692261-75712662	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs7975661	GLIPR1L2	cis	parietal	SCAN
rs7975661	GLIPR1L1	cis	lymphoblastoid	seeQTL
rs7975661	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs7975661	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs7975661	GLIPR1L2	cis	Artery Tibial	GTEx
rs7975661	GLIPR1L2	cis	Heart Left Ventricle	GTEx
rs7975661	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs7975661	GLIPR1	cis	parietal	SCAN
rs7975661	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs7975661	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs7975661	GLIPR1L2	cis	Nerve Tibial	GTEx
rs7975661	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs7975661	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs7975661	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7975661	GLIPR1L2	cis	cerebellum	SCAN
rs7975661	KRR1	cis	parietal	SCAN
rs7975661	RP11-585P4.5	cis	Thyroid	GTEx
rs7975661	GLIPR1L2	cis	Artery Aorta	GTEx
rs7975661	GLIPR1L2	cis	Thyroid	GTEx
rs7975661	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs7975661	RP11-585P4.5	cis	Artery Tibial	GTEx
rs7975661	GLIPR1L2	cis	lung	GTEx
rs7975661	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs7975661	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs7975661	GLIPR1L2	cis	Stomach	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75679600-75699200	Weak transcription	Aorta	Aorta
2	chr12:75681200-75711400	Weak transcription	Psoas Muscle	Psoas
3	chr12:75682200-75699200	Weak transcription	Right Ventricle	heart
4	chr12:75682600-75699200	Weak transcription	Left Ventricle	heart
5	chr12:75683400-75697200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:75689800-75697200	Weak transcription	Adipose Nuclei	Adipose
7	chr12:75690200-75699400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:75690600-75697200	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:75691000-75699600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:75691600-75697200	Weak transcription	Brain Anterior Caudate	brain
11	chr12:75691800-75699400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:75692400-75699200	Weak transcription	Ovary	ovary
13	chr12:75695000-75696800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:75695200-75697600	Weak transcription	Liver	Liver
15	chr12:75695400-75699200	Weak transcription	Pancreas	Pancrea
16	chr12:75696000-75706000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:75696200-75698800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:75696200-75699200	Weak transcription	Lung	lung
19	chr12:75696200-75706000	Weak transcription	Esophagus	oesophagus
20	chr12:75696400-75706800	Weak transcription	Brain Angular Gyrus	brain

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