Variant report

Variant	rs57659864
Chromosome Location	chr19:52793115-52793116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52792263..52794621-chr19:52796149..52799005,2	K562	blood:
2	chr19:52773000..52774618-chr19:52792454..52794386,2	K562	blood:
3	chr19:52778691..52781131-chr19:52791731..52793541,2	MCF-7	breast:
4	chr19:52792080..52795278-chr19:52800524..52804050,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198464	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000269102	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10409096	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409142	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409486	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410297	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10411111	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411297	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416012	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418429	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423935	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426029	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462567	1.00[EUR][1000 genomes]
rs12462608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28480595	0.88[ASN][1000 genomes]
rs28485851	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28516831	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28550473	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584863	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665950	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28720915	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34027972	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810122	1.00[ASN][1000 genomes]
rs55739718	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798076	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55910520	0.89[EUR][1000 genomes]
rs55995319	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57659523	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59264782	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60315031	1.00[ASN][1000 genomes]
rs62110413	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110414	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110443	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110446	1.00[EUR][1000 genomes]
rs73577187	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73579004	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73934405	1.00[ASN][1000 genomes]
rs8100167	1.00[EUR][1000 genomes]
rs8100504	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100650	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103205	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103336	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
3	chr19:52774600-52795800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:52777200-52794000	Weak transcription	Psoas Muscle	Psoas
5	chr19:52780400-52800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:52781600-52793600	Weak transcription	Fetal Heart	heart
7	chr19:52783200-52794800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr19:52783200-52795200	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr19:52783400-52795800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
10	chr19:52784400-52794800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:52784600-52794000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:52784600-52794600	ZNF genes & repeats	Primary T cells from cord blood	blood
13	chr19:52784600-52795000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
14	chr19:52784600-52795800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:52784600-52796000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:52784600-52796400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:52784600-52796800	ZNF genes & repeats	Liver	Liver
18	chr19:52784800-52793400	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr19:52784800-52794800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr19:52784800-52795800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:52784800-52795800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:52784800-52795800	Strong transcription	Dnd41	blood
23	chr19:52785000-52793600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr19:52785000-52795400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
25	chr19:52785000-52795800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:52785000-52796000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:52785200-52794600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:52785200-52794800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:52785200-52795400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr19:52785200-52796000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:52785200-52796400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:52785400-52794200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:52785400-52794400	ZNF genes & repeats	Lung	lung
34	chr19:52785400-52795400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:52785400-52796000	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr19:52785400-52796000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:52785400-52796400	Strong transcription	Adipose Nuclei	Adipose
38	chr19:52785400-52797400	Strong transcription	Brain Germinal Matrix	brain
39	chr19:52785600-52795800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:52785800-52793600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:52786000-52796000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr19:52786600-52794800	Strong transcription	Osteobl	bone
43	chr19:52787000-52797000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:52787200-52794600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:52788000-52796200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:52788400-52799800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:52788600-52793400	Weak transcription	NH-A	brain
48	chr19:52788800-52793200	Weak transcription	Brain Angular Gyrus	brain
49	chr19:52788800-52800000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:52789000-52793200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links