Variant report

Variant	rs7560182
Chromosome Location	chr2:100293110-100293111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10167100	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10182731	0.82[EUR][1000 genomes]
rs10183116	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10185240	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10189976	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10205134	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123791	0.87[EUR][1000 genomes]
rs11123792	0.87[EUR][1000 genomes]
rs11676683	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13400157	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13431170	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13431191	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1524366	0.87[EUR][1000 genomes]
rs1916959	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2030689	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2177540	0.89[ASN][1000 genomes]
rs2309724	0.89[ASN][1000 genomes]
rs2309725	0.89[ASN][1000 genomes]
rs4325808	0.80[ASN][1000 genomes]
rs4410333	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611689	0.87[EUR][1000 genomes]
rs4850911	0.86[EUR][1000 genomes]
rs4850912	0.87[EUR][1000 genomes]
rs4850913	0.83[ASN][1000 genomes]
rs6542886	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542889	0.89[ASN][1000 genomes]
rs6709165	0.87[EUR][1000 genomes]
rs6719965	0.87[EUR][1000 genomes]
rs6720070	0.86[EUR][1000 genomes]
rs6734773	0.87[EUR][1000 genomes]
rs6758962	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72817062	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557598	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7566953	0.87[EUR][1000 genomes]
rs870560	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308828	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9679019	0.87[EUR][1000 genomes]

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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7560182	TMEM131	cis	cerebellum	SCAN
rs7560182	LYG1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100253200-100308800	Weak transcription	Gastric	stomach
2	chr2:100257600-100308600	Weak transcription	Thymus	Thymus
3	chr2:100264000-100328600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:100274200-100297400	Weak transcription	Liver	Liver
5	chr2:100276400-100302000	Weak transcription	Left Ventricle	heart
6	chr2:100276600-100295800	Weak transcription	Right Atrium	heart
7	chr2:100279400-100295000	Weak transcription	Fetal Brain Male	brain
8	chr2:100282600-100308600	Weak transcription	Ovary	ovary
9	chr2:100286000-100294000	Weak transcription	Fetal Brain Female	brain
10	chr2:100286000-100297800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:100286000-100301000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:100286000-100305600	Weak transcription	Fetal Thymus	thymus
13	chr2:100286600-100336800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:100287000-100298200	Weak transcription	Dnd41	blood
15	chr2:100288400-100296800	Weak transcription	NH-A	brain
16	chr2:100288800-100302200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:100289000-100300400	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:100289400-100295600	Weak transcription	Fetal Heart	heart
19	chr2:100289800-100296400	Weak transcription	Fetal Lung	lung
20	chr2:100290200-100305000	Strong transcription	Primary B cells from cord blood	blood
21	chr2:100290400-100298800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:100290600-100304800	Weak transcription	Fetal Kidney	kidney
23	chr2:100290800-100293400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:100291200-100310800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:100291400-100295400	Weak transcription	Primary T cells from cord blood	blood
26	chr2:100291600-100307800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr2:100292000-100295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:100292000-100295800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:100292200-100293200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:100292800-100293400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:100293000-100294000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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