Variant report

Variant	rs28845817
Chromosome Location	chr19:52808717-52808718
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	chr19:52800534..52802484-chr19:52807746..52810070,2	MCF-7	breast:
2	chr19:52804812..52807578-chr19:52808701..52812079,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269102	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11880474	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110448	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62110449	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62110450	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8103072	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8103182	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv912299	chr19:52795985-52832830	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52801200-52813200	ZNF genes & repeats	A549	lung
2	chr19:52801600-52808800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:52801800-52827200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:52801800-52829200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:52802000-52808800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:52802000-52813200	ZNF genes & repeats	Primary B cells from cord blood	blood
7	chr19:52802000-52826400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:52802000-52830000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:52802200-52808800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:52802200-52809000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr19:52802200-52813000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
12	chr19:52802200-52827400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:52802200-52828400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:52802200-52829200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr19:52802400-52808800	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:52802400-52814000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
17	chr19:52802400-52828800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
19	chr19:52802600-52826800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr19:52802600-52827600	ZNF genes & repeats	Dnd41	blood
21	chr19:52802800-52809400	Weak transcription	Fetal Heart	heart
22	chr19:52803000-52809200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:52803200-52812400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:52803400-52813200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
25	chr19:52803800-52816200	ZNF genes & repeats	Small Intestine	intestine
26	chr19:52803800-52829000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
27	chr19:52803800-52829200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr19:52804000-52813000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:52804000-52814000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr19:52804400-52808800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:52804400-52827200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
32	chr19:52804600-52809200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:52804800-52809800	Weak transcription	Hela-S3	cervix
34	chr19:52805000-52808800	Weak transcription	Aorta	Aorta
35	chr19:52805000-52819000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr19:52805200-52809000	Weak transcription	HMEC	breast
37	chr19:52805200-52829000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
38	chr19:52805400-52809200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:52805400-52813200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
40	chr19:52805400-52829200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:52805600-52813800	ZNF genes & repeats	Adipose Nuclei	Adipose
42	chr19:52805600-52827800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:52805800-52813800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
44	chr19:52806000-52809200	Weak transcription	Gastric	stomach
45	chr19:52806000-52813200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
46	chr19:52806200-52808800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:52806200-52808800	Weak transcription	Pancreas	Pancrea
48	chr19:52806600-52810000	Weak transcription	Osteobl	bone
49	chr19:52806800-52809000	Weak transcription	HUVEC	blood vessel
50	chr19:52806800-52809200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links