Variant report

Variant	rs4568000
Chromosome Location	chr2:100225347-100225348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100219395..100221538-chr2:100225234..100227761,2	K562	blood:
2	chr2:100224603..100226583-chr2:100228507..100231236,2	MCF-7	breast:
3	chr2:100190593..100193147-chr2:100224653..100226981,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10167100	0.80[AMR][1000 genomes]
rs11123789	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895560	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900988	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901863	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12474603	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12612124	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12616127	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712052	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309728	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34112064	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792128	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4611689	0.80[AMR][1000 genomes]
rs4850908	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55989048	0.88[ASN][1000 genomes]
rs6716694	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6722898	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558495	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561197	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561948	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7567996	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9973326	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9973472	0.86[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
rs4568000	LYG1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100211000-100234200	Weak transcription	Thymus	Thymus
2	chr2:100211000-100249600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:100215400-100232000	Weak transcription	Lung	lung
4	chr2:100217000-100258400	Weak transcription	Primary T cells from cord blood	blood
5	chr2:100218200-100226400	Weak transcription	Right Atrium	heart
6	chr2:100218200-100229200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:100218200-100241400	Weak transcription	Spleen	Spleen
8	chr2:100224000-100225600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:100224400-100226400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:100224400-100231600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:100224800-100226400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:100224800-100230400	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:100224800-100230400	Weak transcription	HSMMtube	muscle
14	chr2:100224800-100237800	Weak transcription	Fetal Lung	lung
15	chr2:100224800-100239800	Weak transcription	Right Ventricle	heart
16	chr2:100225000-100226000	Weak transcription	K562	blood
17	chr2:100225000-100227200	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:100225000-100229000	Weak transcription	Fetal Brain Female	brain
19	chr2:100225000-100231600	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:100225200-100225400	Enhancers	Osteobl	bone
21	chr2:100225200-100225600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:100225200-100226000	Weak transcription	Primary B cells from cord blood	blood
23	chr2:100225200-100226400	Weak transcription	Fetal Brain Male	brain
24	chr2:100225200-100230800	Weak transcription	Fetal Muscle Leg	muscle

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