Variant report

Variant	rs7258953
Chromosome Location	chr19:44353454-44353455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44352671..44354386-chr19:44358392..44361083,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10407794	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12459186	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1865108	0.80[CEU][hapmap]
rs189445	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2033492	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2195980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239947	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs349026	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs349027	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs349031	0.94[ASN][1000 genomes]
rs349035	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs349036	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs349037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs349056	0.80[ASN][1000 genomes]
rs443389	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7251009	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv458710	chr19:44339960-44410846	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv579853	chr19:44339960-44410846	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv524460	chr19:44352688-44372015	Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44332800-44357200	ZNF genes & repeats	Liver	Liver
2	chr19:44333600-44357400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:44335200-44357200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:44335200-44368200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:44335400-44357200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:44335400-44366600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:44336600-44357600	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr19:44336800-44356800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
9	chr19:44336800-44357200	ZNF genes & repeats	Fetal Lung	lung
10	chr19:44339000-44355400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
11	chr19:44339200-44355400	ZNF genes & repeats	Primary B cells from cord blood	blood
12	chr19:44339200-44355400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
13	chr19:44339200-44357200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:44339400-44355400	ZNF genes & repeats	Primary T cells from cord blood	blood
15	chr19:44339400-44355600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:44339600-44355400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
17	chr19:44341000-44354200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
18	chr19:44341000-44355400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr19:44341000-44357200	ZNF genes & repeats	Brain Anterior Caudate	brain
20	chr19:44341200-44354800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr19:44341200-44357200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:44342200-44355400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
23	chr19:44345800-44355400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
24	chr19:44347600-44354600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:44347600-44354600	Weak transcription	Fetal Stomach	stomach
26	chr19:44348600-44355400	ZNF genes & repeats	HSMM	muscle
27	chr19:44348600-44357000	ZNF genes & repeats	Fetal Brain Female	brain
28	chr19:44349200-44357200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:44349800-44354600	ZNF genes & repeats	Fetal Heart	heart
30	chr19:44349800-44355200	ZNF genes & repeats	NHEK	skin
31	chr19:44350000-44354000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr19:44350400-44354000	ZNF genes & repeats	NHDF-Ad	bronchial
33	chr19:44350400-44355200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
34	chr19:44350400-44355600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:44350400-44355600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr19:44350400-44355800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
37	chr19:44350400-44356200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:44350400-44357000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr19:44350400-44357200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
40	chr19:44350600-44355000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:44350600-44355200	ZNF genes & repeats	Colon Smooth Muscle	Colon
42	chr19:44350600-44355400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
43	chr19:44350600-44355400	ZNF genes & repeats	Brain Angular Gyrus	brain
44	chr19:44350600-44355400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
45	chr19:44350600-44355400	ZNF genes & repeats	Brain Substantia Nigra	brain
46	chr19:44350600-44355400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
47	chr19:44350600-44355400	ZNF genes & repeats	A549	lung
48	chr19:44350600-44355400	ZNF genes & repeats	HSMMtube	muscle
49	chr19:44350600-44355400	ZNF genes & repeats	Osteobl	bone
50	chr19:44350600-44355600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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