Variant report

Variant	rs58378377
Chromosome Location	chr2:100216599-100216600
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100203483..100206478-chr2:100214473..100216979,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10514778	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17765792	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17782372	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17782408	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58345533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59396573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60357076	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60695941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61379087	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62154470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154482	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62154484	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62154485	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62154487	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62154492	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62154519	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154521	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154522	0.89[AMR][1000 genomes]
rs62154524	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154526	0.85[EUR][1000 genomes]
rs62154528	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154529	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154530	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154533	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154535	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154536	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154538	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62154540	0.82[EUR][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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100162800-100219200	Strong transcription	Primary B cells from peripheral blood	blood
2	chr2:100190400-100218200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:100199400-100217800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:100203200-100221400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:100203400-100221200	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:100203800-100217200	Weak transcription	Liver	Liver
7	chr2:100204000-100217400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:100204000-100218000	Weak transcription	Fetal Lung	lung
9	chr2:100204000-100221800	Weak transcription	Adipose Nuclei	Adipose
10	chr2:100207800-100219800	Strong transcription	Primary B cells from cord blood	blood
11	chr2:100210400-100218400	Weak transcription	Dnd41	blood
12	chr2:100210400-100219800	Weak transcription	Gastric	stomach
13	chr2:100210600-100217600	Weak transcription	Spleen	Spleen
14	chr2:100210600-100224200	Weak transcription	Brain Germinal Matrix	brain
15	chr2:100210800-100216800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:100211000-100219000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:100211000-100234200	Weak transcription	Thymus	Thymus
18	chr2:100211000-100249600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:100211600-100219800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:100212800-100221400	Weak transcription	Ovary	ovary
21	chr2:100213000-100218000	Weak transcription	Fetal Brain Female	brain
22	chr2:100213200-100216800	Weak transcription	Fetal Brain Male	brain
23	chr2:100214800-100217400	Weak transcription	Osteobl	bone
24	chr2:100214800-100217600	Weak transcription	NH-A	brain
25	chr2:100215000-100217400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:100215000-100217800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:100215200-100217600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:100215200-100217800	Weak transcription	HSMM	muscle
29	chr2:100215400-100216600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:100215400-100216600	Weak transcription	Primary T cells from cord blood	blood
31	chr2:100215400-100217600	Weak transcription	Fetal Kidney	kidney
32	chr2:100215400-100217800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:100215400-100218000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr2:100215400-100218000	Weak transcription	HSMMtube	muscle
35	chr2:100215400-100232000	Weak transcription	Lung	lung
36	chr2:100215600-100216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:100215600-100217600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:100215800-100217600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:100216000-100218000	Weak transcription	Fetal Heart	heart
40	chr2:100216400-100216800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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