Variant report

Variant	rs11123789
Chromosome Location	chr2:100223694-100223695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11895560	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900988	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901863	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12474603	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12612124	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12616127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712052	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1916959	0.83[AMR][1000 genomes]
rs2309728	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34112064	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792128	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4568000	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850908	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55989048	0.88[ASN][1000 genomes]
rs6716694	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6722898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558495	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561197	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561948	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7567996	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9973326	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9973472	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11123789	LYG1	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100210600-100224200	Weak transcription	Brain Germinal Matrix	brain
2	chr2:100211000-100234200	Weak transcription	Thymus	Thymus
3	chr2:100211000-100249600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:100215400-100232000	Weak transcription	Lung	lung
5	chr2:100217000-100258400	Weak transcription	Primary T cells from cord blood	blood
6	chr2:100218200-100226400	Weak transcription	Right Atrium	heart
7	chr2:100218200-100229200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:100218200-100241400	Weak transcription	Spleen	Spleen
9	chr2:100218800-100224200	Weak transcription	Fetal Brain Female	brain
10	chr2:100219200-100225000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:100219800-100224000	Weak transcription	Primary B cells from cord blood	blood
12	chr2:100219800-100224400	Weak transcription	HSMMtube	muscle
13	chr2:100221200-100224800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:100221400-100224200	Weak transcription	K562	blood
15	chr2:100222200-100224000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:100222200-100224000	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:100222200-100224200	Weak transcription	Adipose Nuclei	Adipose
18	chr2:100222200-100224200	Weak transcription	Fetal Lung	lung
19	chr2:100222200-100224400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:100222200-100225200	Weak transcription	Osteobl	bone
21	chr2:100222400-100224000	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:100222800-100225200	Enhancers	Fetal Brain Male	brain
23	chr2:100223000-100224000	Weak transcription	Ovary	ovary
24	chr2:100223200-100224000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:100223600-100223800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:100223600-100224200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:100223600-100224400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:100223600-100224800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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