Variant report

Variant	rs17140890
Chromosome Location	chr7:69240249-69240250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1003404	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10260553	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10487947	0.84[ASN][1000 genomes]
rs12670658	0.89[ASN][1000 genomes]
rs1548748	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1990444	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs210602	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs210605	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2215354	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2533436	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2533437	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2851486	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2851493	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2851519	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2851520	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34701787	0.89[ASN][1000 genomes]
rs41848	0.89[ASN][1000 genomes]
rs41854	0.89[ASN][1000 genomes]
rs41857	0.89[ASN][1000 genomes]
rs4717522	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs548556	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs569334	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs628885	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs633927	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6953849	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs917617	0.94[AMR][1000 genomes];0.97[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	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17140890	STAG3L4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69233600-69240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:69234800-69245800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:69235800-69242000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:69236200-69242800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:69236200-69243400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:69237400-69240800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:69237400-69246400	Weak transcription	Fetal Lung	lung
8	chr7:69237800-69246400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:69238000-69241000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr7:69238600-69242400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:69238600-69245800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:69238800-69245400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:69238800-69245600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:69238800-69246200	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:69239000-69240600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:69239000-69242000	Weak transcription	GM12878-XiMat	blood
17	chr7:69239000-69242400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:69239000-69245400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:69239000-69245600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr7:69239000-69245800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:69239200-69240600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:69239200-69245000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr7:69239200-69245600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr7:69239400-69240400	Weak transcription	Adipose Nuclei	Adipose
25	chr7:69239600-69241200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:69239800-69240800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:69239800-69241200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:69240000-69240800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:69240000-69240800	Enhancers	HSMMtube	muscle
30	chr7:69240000-69241200	Enhancers	NHDF-Ad	bronchial
31	chr7:69240200-69240600	Enhancers	Esophagus	oesophagus
32	chr7:69240200-69240600	Enhancers	Fetal Muscle Leg	muscle
33	chr7:69240200-69240600	Enhancers	Fetal Stomach	stomach
34	chr7:69240200-69240600	Enhancers	Rectal Smooth Muscle	rectum
35	chr7:69240200-69240600	Enhancers	HSMM	muscle
36	chr7:69240200-69240800	Enhancers	Fetal Muscle Trunk	muscle
37	chr7:69240200-69240800	Enhancers	Left Ventricle	heart
38	chr7:69240200-69240800	Enhancers	Ovary	ovary
39	chr7:69240200-69240800	Enhancers	Psoas Muscle	Psoas
40	chr7:69240200-69240800	Enhancers	Right Ventricle	heart
41	chr7:69240200-69240800	Enhancers	NHEK	skin
42	chr7:69240200-69241000	Enhancers	Colon Smooth Muscle	Colon
43	chr7:69240200-69241000	Enhancers	A549	lung
44	chr7:69240200-69241000	Enhancers	NH-A	brain
45	chr7:69240200-69241200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:69240200-69241200	Enhancers	Right Atrium	heart
47	chr7:69240200-69241200	Enhancers	Osteobl	bone
48	chr7:69240200-69241400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:69240200-69241400	Enhancers	Fetal Heart	heart
50	chr7:69240200-69242800	Enhancers	Placenta	Placenta

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