Variant report

Variant	rs28516831
Chromosome Location	chr19:52795131-52795132
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52793468..52795299-chr19:52799350..52801960,2	MCF-7	breast:
2	chr19:52792080..52795278-chr19:52800524..52804050,3	MCF-7	breast:
3	chr19:52786877..52789123-chr19:52793597..52795383,2	K562	blood:

Variant related genes	Relation type
ENSG00000198464	Chromatin interaction
ENSG00000269102	Chromatin interaction

Extended variants
information (count: 47 )
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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10411111	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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418429	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423935	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426029	1.00[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	0.96[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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28550473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584863	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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34027972	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	0.83[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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57659864	0.95[AFR][1000 genomes];1.00[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	0.83[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:7 , 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
6	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 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	chr19:52780400-52800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:52783200-52795200	ZNF genes & repeats	Fetal Intestine Small	intestine
6	chr19:52783400-52795800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
7	chr19:52784600-52795800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr19:52784600-52796000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:52784600-52796400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:52784600-52796800	ZNF genes & repeats	Liver	Liver
11	chr19:52784800-52795800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:52784800-52795800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:52784800-52795800	Strong transcription	Dnd41	blood
14	chr19:52785000-52795400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
15	chr19:52785000-52795800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr19:52785000-52796000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:52785200-52795400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:52785200-52796000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:52785200-52796400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:52785400-52795400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:52785400-52796000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr19:52785400-52796000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:52785400-52796400	Strong transcription	Adipose Nuclei	Adipose
24	chr19:52785400-52797400	Strong transcription	Brain Germinal Matrix	brain
25	chr19:52785600-52795800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr19:52786000-52796000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:52787000-52797000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:52788000-52796200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:52788400-52799800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:52788800-52800000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:52789200-52795800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:52789200-52799400	Weak transcription	Pancreas	Pancrea
33	chr19:52790800-52796400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:52791400-52795400	Strong transcription	Fetal Brain Female	brain
35	chr19:52791400-52795600	Strong transcription	Placenta	Placenta
36	chr19:52791400-52795800	Strong transcription	Ovary	ovary
37	chr19:52791600-52795400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:52791600-52795800	Strong transcription	HSMMtube	muscle
39	chr19:52791800-52799600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:52792200-52800400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr19:52792600-52795800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr19:52792600-52796000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:52792600-52797800	ZNF genes & repeats	A549	lung
44	chr19:52792800-52795600	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr19:52792800-52795800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
46	chr19:52792800-52795800	ZNF genes & repeats	Thymus	Thymus
47	chr19:52793200-52795800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
48	chr19:52793200-52796000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:52793400-52796000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:52793600-52795200	Strong transcription	Fetal Lung	lung

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