Variant report

Variant	rs17156078
Chromosome Location	chr7:27988689-27988690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10486564	1.00[CEU][hapmap];0.91[MEX][hapmap]
rs10486567	0.95[LWK][hapmap]
rs1557779	0.84[ASW][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs16874408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17156032	1.00[CEU][hapmap]
rs17156080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56901033	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6968704	0.85[LWK][hapmap]
rs73299490	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73299499	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17156078	PTGS2	trans	brain	seeQTL
rs17156078	HBG2	trans	brain	seeQTL
rs17156078	CCL4	trans	brain	seeQTL
rs17156078	GADD45G	trans	brain	seeQTL
rs17156078	HBG1	trans	brain	seeQTL
rs17156078	FOSB	trans	brain	seeQTL
rs17156078	EGR4	trans	brain	seeQTL
rs17156078	FABP4	trans	brain	seeQTL
rs17156078	EGR2	trans	brain	seeQTL
rs17156078	ZNF331	trans	brain	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
2	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr7:27957600-28000800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:27974000-27990800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:27976600-27991600	Weak transcription	Osteobl	bone
6	chr7:27977000-28001400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:27977400-27991600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:27978600-27993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:27979200-28000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:27980200-28000000	Weak transcription	Lung	lung
11	chr7:27980400-27988800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:27980400-28000000	Weak transcription	Pancreas	Pancrea
13	chr7:27980400-28017200	Weak transcription	Aorta	Aorta
14	chr7:27980600-27993400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr7:27982200-27989400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:27983200-27989600	Enhancers	Fetal Heart	heart
17	chr7:27983400-27989200	Enhancers	Colon Smooth Muscle	Colon
18	chr7:27983600-27989000	Enhancers	Rectal Smooth Muscle	rectum
19	chr7:27984200-27989800	Enhancers	HSMMtube	muscle
20	chr7:27985000-27990200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:27985600-27991200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:27986000-27988800	Enhancers	Brain Angular Gyrus	brain
23	chr7:27986000-27989400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr7:27986200-27989000	Enhancers	Brain Cingulate Gyrus	brain
25	chr7:27986200-27989000	Weak transcription	Psoas Muscle	Psoas
26	chr7:27986600-27991400	Weak transcription	Adipose Nuclei	Adipose
27	chr7:27986600-27991600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr7:27987200-27988800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr7:27987200-27988800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:27987200-27989200	Enhancers	HSMM	muscle
31	chr7:27987200-27990200	Enhancers	Fetal Muscle Leg	muscle
32	chr7:27987400-27989000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:27987600-27990800	Weak transcription	Brain Anterior Caudate	brain
34	chr7:27987800-27988800	Weak transcription	Right Ventricle	heart
35	chr7:27987800-27990200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr7:27987800-27991400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:27987800-27991400	Weak transcription	NHDF-Ad	bronchial
38	chr7:27987800-27991600	Weak transcription	Fetal Stomach	stomach
39	chr7:27987800-27992400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:27987800-27993400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:27987800-27998200	Weak transcription	Ovary	ovary
42	chr7:27987800-27999600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:27988000-27991600	Weak transcription	Right Atrium	heart
44	chr7:27988200-27990600	Enhancers	Brain Substantia Nigra	brain
45	chr7:27988200-27991400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:27988400-27990000	Strong transcription	Primary B cells from cord blood	blood
47	chr7:27988400-27990200	Enhancers	Left Ventricle	heart
48	chr7:27988600-27988800	Enhancers	Fetal Muscle Trunk	muscle
49	chr7:27988600-27989600	Weak transcription	Brain Hippocampus Middle	brain

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