Variant report

Variant	rs62154530
Chromosome Location	chr2:100254714-100254715
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100231861..100234542-chr2:100254198..100256045,2	MCF-7	breast:
2	chr2:100251850..100255492-chr2:100257476..100259432,3	K562	blood:
3	chr2:100193349..100195395-chr2:100253004..100255403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144218	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514778	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17765792	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782372	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782408	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782756	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58345533	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58378377	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59396573	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60357076	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60695941	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61379087	0.85[EUR][1000 genomes]
rs62154468	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154470	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154476	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154482	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62154484	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62154485	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62154487	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62154492	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62154519	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154521	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154524	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154526	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154528	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154529	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62154533	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154535	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62154536	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154538	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154540	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62154559	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100217000-100258400	Weak transcription	Primary T cells from cord blood	blood
2	chr2:100239600-100257200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:100251800-100258400	Enhancers	Fetal Muscle Leg	muscle
4	chr2:100252000-100254800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:100252000-100255200	Enhancers	Fetal Muscle Trunk	muscle
6	chr2:100252000-100256600	Enhancers	Fetal Thymus	thymus
7	chr2:100252400-100263800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:100253200-100254800	Weak transcription	Dnd41	blood
9	chr2:100253200-100255000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:100253200-100255800	Enhancers	Primary B cells from cord blood	blood
11	chr2:100253200-100308800	Weak transcription	Gastric	stomach
12	chr2:100253600-100256000	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:100253600-100257200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:100253600-100257200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:100253600-100260000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:100253600-100260400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:100253600-100260400	Weak transcription	Psoas Muscle	Psoas
18	chr2:100253600-100260600	Weak transcription	Brain Substantia Nigra	brain
19	chr2:100253800-100256400	Weak transcription	Ovary	ovary
20	chr2:100253800-100257400	Weak transcription	Fetal Lung	lung
21	chr2:100253800-100257400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:100253800-100260400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:100254000-100255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:100254000-100255000	Weak transcription	Pancreas	Pancrea
25	chr2:100254000-100256600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:100254000-100256600	Weak transcription	Fetal Heart	heart
27	chr2:100254000-100257200	Weak transcription	Left Ventricle	heart
28	chr2:100254000-100257400	Weak transcription	Right Ventricle	heart
29	chr2:100254000-100259800	Weak transcription	Brain Germinal Matrix	brain
30	chr2:100254000-100260000	Weak transcription	Right Atrium	heart
31	chr2:100254000-100260400	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:100254000-100265000	Weak transcription	Spleen	Spleen
33	chr2:100254200-100257200	Weak transcription	Fetal Brain Female	brain
34	chr2:100254200-100257200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:100254400-100255400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:100254400-100256800	Weak transcription	Fetal Kidney	kidney
37	chr2:100254400-100256800	Weak transcription	HSMMtube	muscle
38	chr2:100254400-100260000	Weak transcription	Adipose Nuclei	Adipose
39	chr2:100254600-100255200	Flanking Active TSS	Thymus	Thymus
40	chr2:100254600-100258200	Weak transcription	Fetal Brain Male	brain

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