Variant report

Variant	rs279673
Chromosome Location	chr7:121752006-121752007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10464523	1.00[CHD][hapmap]
rs1196479	1.00[JPT][hapmap]
rs1196489	1.00[JPT][hapmap]
rs1196509	1.00[JPT][hapmap]
rs1206361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1206362	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1206371	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1206372	0.82[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1206375	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1206378	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1206491	1.00[JPT][hapmap]
rs1206496	1.00[JPT][hapmap]
rs1206498	1.00[JPT][hapmap]
rs1206499	1.00[JPT][hapmap]
rs12706384	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13223149	0.98[EUR][1000 genomes]
rs13225749	0.81[GIH][hapmap]
rs13232539	1.00[EUR][1000 genomes]
rs1405236	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1405237	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1725067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2215358	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs279665	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs279670	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs279676	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs279679	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs279680	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs279689	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs279700	0.82[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs279701	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs279707	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3757542	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427803	chr7:121701581-121876302	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1019004	chr7:121733372-121800380	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1034553	chr7:121734934-121800380	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv608335	chr7:121749963-121779485	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs279673	GNG11	trans	lymphoblastoid	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:121685000-121772000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:121703400-121755800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:121716000-121772000	Weak transcription	Osteobl	bone
4	chr7:121716000-121775600	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:121716200-121758200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:121718000-121754200	Weak transcription	Placenta	Placenta
7	chr7:121718000-121754600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:121718000-121754800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:121718000-121756200	Weak transcription	Pancreas	Pancrea
10	chr7:121718200-121755000	Weak transcription	NHDF-Ad	bronchial
11	chr7:121722000-121755000	Weak transcription	HUVEC	blood vessel
12	chr7:121725800-121758400	Weak transcription	HSMMtube	muscle
13	chr7:121726000-121774400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:121726000-121776000	Weak transcription	Fetal Stomach	stomach
15	chr7:121730400-121754600	Weak transcription	Aorta	Aorta
16	chr7:121731800-121753600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:121731800-121770400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:121732000-121773600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr7:121739800-121760400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:121742200-121753400	Weak transcription	HSMM	muscle
21	chr7:121742600-121754200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:121742600-121756200	Weak transcription	Right Ventricle	heart
23	chr7:121743000-121770200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:121743800-121776200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr7:121744600-121753200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:121744600-121783200	Weak transcription	Lung	lung
27	chr7:121744800-121754400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:121744800-121760400	Strong transcription	Liver	Liver
29	chr7:121744800-121775200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:121744800-121776800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr7:121745600-121774000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:121746600-121754200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:121747200-121757000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:121747200-121762400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:121747600-121754600	Weak transcription	Ovary	ovary
36	chr7:121747800-121753000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:121747800-121755000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:121747800-121756200	Weak transcription	Brain Angular Gyrus	brain
39	chr7:121747800-121756200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:121747800-121760000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr7:121747800-121760000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr7:121747800-121775800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:121747800-121776200	Weak transcription	Fetal Brain Male	brain
44	chr7:121748000-121755400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:121748000-121755600	Weak transcription	Brain Anterior Caudate	brain
46	chr7:121748200-121763600	Weak transcription	HMEC	breast
47	chr7:121748400-121752400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr7:121749600-121752200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:121749600-121752400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:121749600-121753600	Weak transcription	Brain Substantia Nigra	brain

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