Variant report

Variant	rs10153500
Chromosome Location	chr19:38073267-38073268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38071504..38073615-chr19:38074702..38076775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180479	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1038084	0.95[YRI][hapmap]
rs10407657	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs10424047	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10424612	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs11083424	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[MEX][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs11879149	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11880056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11880604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11883255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2927743	0.85[YRI][hapmap]
rs2927744	1.00[YRI][hapmap]
rs34206817	0.97[EUR][1000 genomes]
rs34743484	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3745763	1.00[CEU][hapmap]
rs3810359	0.85[ASN][1000 genomes]
rs45505797	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802069	1.00[YRI][hapmap]
rs4803216	0.95[YRI][hapmap]
rs56075341	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56264690	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56281742	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57504517	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57725815	0.90[EUR][1000 genomes]
rs57867853	0.97[EUR][1000 genomes]
rs59966837	0.97[EUR][1000 genomes]
rs60686304	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108262	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108264	0.85[ASN][1000 genomes]
rs62108289	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108290	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108292	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108293	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108297	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62108344	0.82[AFR][1000 genomes]
rs62108348	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62108354	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62110178	0.97[EUR][1000 genomes]
rs62110183	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62110185	0.90[EUR][1000 genomes]
rs62110186	0.90[EUR][1000 genomes]
rs62110187	0.81[EUR][1000 genomes]
rs62111488	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62111490	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7245981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7247175	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7254780	1.00[CEU][hapmap]
rs7255283	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs7255938	1.00[CEU][hapmap]
rs7256747	0.80[AFR][1000 genomes]
rs7258992	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7259029	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7259272	0.88[CHB][hapmap];0.95[CHD][hapmap]
rs7259321	0.82[AMR][1000 genomes]
rs7259717	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73930999	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73932929	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73932955	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8101991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8102189	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8104124	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8104747	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8108261	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8113076	0.95[YRI][hapmap];0.81[AFR][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	esv3374404	chr19:38072959-38073379	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38032400-38080800	ZNF genes & repeats	Liver	Liver
2	chr19:38032600-38075200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:38038000-38078400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:38038600-38079600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:38041200-38079600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38045000-38078600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:38046600-38079600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
8	chr19:38047400-38078600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
9	chr19:38049200-38079600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr19:38051600-38077600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:38051600-38078800	ZNF genes & repeats	Fetal Brain Female	brain
12	chr19:38052200-38075200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr19:38052200-38078600	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr19:38053200-38078200	ZNF genes & repeats	Brain Germinal Matrix	brain
15	chr19:38053200-38078600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:38053400-38078400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
17	chr19:38059800-38078000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr19:38065200-38078800	ZNF genes & repeats	Colon Smooth Muscle	Colon
19	chr19:38065800-38078400	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr19:38065800-38078600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr19:38067000-38077200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:38068200-38078200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
23	chr19:38068400-38073400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
24	chr19:38068400-38078000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
25	chr19:38068400-38078200	ZNF genes & repeats	Fetal Muscle Leg	muscle
26	chr19:38068400-38078400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:38068400-38078600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:38068400-38078800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
29	chr19:38068600-38075000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:38068600-38075000	ZNF genes & repeats	Thymus	Thymus
31	chr19:38068600-38076600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
32	chr19:38068600-38077600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
33	chr19:38068600-38078200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
34	chr19:38068600-38078400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:38068600-38080000	ZNF genes & repeats	Ovary	ovary
36	chr19:38068600-38080800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr19:38068800-38075000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:38068800-38075200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:38068800-38075200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:38068800-38078200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
41	chr19:38068800-38079800	ZNF genes & repeats	Dnd41	blood
42	chr19:38069200-38079600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr19:38069400-38073600	Strong transcription	Right Ventricle	heart
44	chr19:38069600-38077800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
45	chr19:38069800-38084600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:38070000-38075200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:38070200-38075200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:38070200-38076200	Weak transcription	Stomach Mucosa	stomach
49	chr19:38070400-38077800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:38070400-38079600	ZNF genes & repeats	Fetal Lung	lung

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