Variant report

Variant	rs2571162
Chromosome Location	chr19:44950933-44950934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44943302..44945039-chr19:44949039..44951597,2	MCF-7	breast:
2	chr19:44945678..44948451-chr19:44948958..44951509,3	MCF-7	breast:
3	chr19:44699013..44701606-chr19:44950381..44952368,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs17354917	1.00[YRI][hapmap]
rs2466416	0.88[ASN][1000 genomes]
rs2571158	0.84[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2571159	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571160	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2571161	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571163	0.90[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs2571164	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571165	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2571166	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571169	0.90[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs2571170	0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571174	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722693	0.96[ASN][1000 genomes]
rs2722697	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722698	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2722699	0.90[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs2722700	0.90[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs2722701	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2722702	0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2734453	0.90[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs2734457	0.96[ASN][1000 genomes]
rs35660276	0.85[CHB][hapmap]
rs4802224	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44928400-44951800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:44932000-44953200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr19:44936000-44951400	Weak transcription	Fetal Heart	heart
4	chr19:44936400-44952000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:44937400-44951800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:44938400-44951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:44938800-44951600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:44940200-44951200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr19:44940600-44951800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:44940600-44951800	Weak transcription	Fetal Thymus	thymus
11	chr19:44942200-44951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:44942400-44951400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:44942600-44952000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:44944400-44952200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr19:44944600-44952200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:44945000-44951200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
17	chr19:44945200-44951200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr19:44945400-44951200	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr19:44945600-44951800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:44945800-44951000	Strong transcription	NHLF	lung
21	chr19:44946200-44951800	Weak transcription	HUVEC	blood vessel
22	chr19:44946400-44951400	ZNF genes & repeats	Brain Germinal Matrix	brain
23	chr19:44946400-44953000	ZNF genes & repeats	Aorta	Aorta
24	chr19:44947000-44951800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr19:44947400-44951200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:44947400-44951400	Weak transcription	Right Ventricle	heart
27	chr19:44947400-44951400	Weak transcription	NHDF-Ad	bronchial
28	chr19:44947800-44951800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:44948200-44951000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr19:44948200-44951600	ZNF genes & repeats	Fetal Lung	lung
31	chr19:44948200-44951800	ZNF genes & repeats	A549	lung
32	chr19:44948200-44959800	ZNF genes & repeats	Liver	Liver
33	chr19:44948400-44951200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
34	chr19:44948400-44951600	Strong transcription	HSMM	muscle
35	chr19:44948400-44952200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:44948600-44951400	Strong transcription	HSMMtube	muscle
37	chr19:44948600-44953200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr19:44948800-44951800	Strong transcription	Fetal Intestine Large	intestine
39	chr19:44948800-44951800	Weak transcription	NH-A	brain
40	chr19:44949400-44951600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr19:44949400-44951600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:44949400-44951600	Weak transcription	Colon Smooth Muscle	Colon
43	chr19:44949600-44951000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
44	chr19:44949600-44951600	ZNF genes & repeats	Psoas Muscle	Psoas
45	chr19:44949600-44954200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
46	chr19:44949800-44951000	ZNF genes & repeats	Brain Substantia Nigra	brain
47	chr19:44949800-44951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:44949800-44951800	ZNF genes & repeats	Primary T cells from cord blood	blood
49	chr19:44950000-44952000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr19:44950200-44951400	Weak transcription	NHEK	skin

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