Variant report

Variant	rs6542884
Chromosome Location	chr2:100258898-100258899
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100256848..100260746-chr2:100260857..100263366,4	K562	blood:
2	chr2:100251850..100255492-chr2:100257476..100259432,3	K562	blood:
3	chr2:100256848..100259824-chr2:100260990..100263145,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10167554	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11123790	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684088	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12620982	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712049	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12712054	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13029690	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1357719	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996984	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2030691	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2030692	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2030693	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2049400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177541	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2177542	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309729	0.80[EUR][1000 genomes]
rs2871316	0.80[EUR][1000 genomes]
rs3792129	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3792130	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3792131	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4850910	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851220	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851221	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6738724	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6745568	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561009	0.80[EUR][1000 genomes]
rs7579222	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9284724	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9308826	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9308827	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9678859	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][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

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100252400-100263800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:100253200-100308800	Weak transcription	Gastric	stomach
3	chr2:100253600-100260000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:100253600-100260400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:100253600-100260400	Weak transcription	Psoas Muscle	Psoas
6	chr2:100253600-100260600	Weak transcription	Brain Substantia Nigra	brain
7	chr2:100253800-100260400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:100254000-100259800	Weak transcription	Brain Germinal Matrix	brain
9	chr2:100254000-100260000	Weak transcription	Right Atrium	heart
10	chr2:100254000-100260400	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:100254000-100265000	Weak transcription	Spleen	Spleen
12	chr2:100254400-100260000	Weak transcription	Adipose Nuclei	Adipose
13	chr2:100255200-100260200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:100255400-100268600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:100255400-100285400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:100255400-100285400	Weak transcription	Dnd41	blood
17	chr2:100256600-100267400	Weak transcription	Fetal Thymus	thymus
18	chr2:100257200-100260600	Weak transcription	Fetal Kidney	kidney
19	chr2:100257600-100259200	Weak transcription	Fetal Brain Female	brain
20	chr2:100257600-100259800	Weak transcription	Fetal Stomach	stomach
21	chr2:100257600-100260000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:100257600-100260000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:100257600-100260400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:100257600-100260400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:100257600-100260600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:100257600-100265000	Weak transcription	Left Ventricle	heart
27	chr2:100257600-100308600	Weak transcription	Thymus	Thymus
28	chr2:100257800-100259200	Strong transcription	Primary B cells from cord blood	blood
29	chr2:100257800-100259800	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:100257800-100260000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:100257800-100260000	Weak transcription	Fetal Lung	lung
32	chr2:100257800-100260000	Weak transcription	Pancreas	Pancrea
33	chr2:100257800-100260200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:100257800-100260400	Weak transcription	Right Ventricle	heart
35	chr2:100257800-100260600	Weak transcription	Fetal Heart	heart
36	chr2:100258200-100260800	Enhancers	Fetal Brain Male	brain
37	chr2:100258400-100259400	Strong transcription	Primary T cells from cord blood	blood
38	chr2:100258400-100260000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:100258800-100259400	Enhancers	Primary B cells from peripheral blood	blood

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