Variant report

Variant	rs28542592
Chromosome Location	chr19:52802969-52802970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2657941	1.00[ASN][1000 genomes]
rs321927	1.00[ASN][1000 genomes]
rs55952017	1.00[ASN][1000 genomes]
rs56014207	0.84[ASN][1000 genomes]
rs62108268	0.92[ASN][1000 genomes]
rs62110456	1.00[ASN][1000 genomes]
rs62110457	1.00[ASN][1000 genomes]
rs62110458	1.00[ASN][1000 genomes]
rs62111460	1.00[ASN][1000 genomes]
rs62111461	1.00[ASN][1000 genomes]
rs7359849	1.00[ASN][1000 genomes]
rs8103810	1.00[ASN][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:117 , 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	chr19:52801400-52803200	Weak transcription	Aorta	Aorta
3	chr19:52801400-52803400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:52801400-52804000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:52801400-52804000	Weak transcription	Hela-S3	cervix
6	chr19:52801600-52803000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:52801600-52803000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:52801600-52803000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:52801600-52803000	Weak transcription	Placenta	Placenta
10	chr19:52801600-52803200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr19:52801600-52803200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:52801600-52803200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:52801600-52803200	Weak transcription	Brain Anterior Caudate	brain
14	chr19:52801600-52803200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:52801600-52803200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr19:52801600-52803200	Weak transcription	Fetal Kidney	kidney
17	chr19:52801600-52803200	Weak transcription	Lung	lung
18	chr19:52801600-52803200	Weak transcription	Pancreas	Pancrea
19	chr19:52801600-52803200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr19:52801600-52803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:52801600-52803400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:52801600-52803400	Weak transcription	Adipose Nuclei	Adipose
23	chr19:52801600-52803400	Weak transcription	Brain Substantia Nigra	brain
24	chr19:52801600-52803400	Weak transcription	Gastric	stomach
25	chr19:52801600-52803400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:52801600-52803400	Weak transcription	HMEC	breast
27	chr19:52801600-52803600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr19:52801600-52803600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:52801600-52803600	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:52801600-52803600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:52801600-52803600	Weak transcription	Right Ventricle	heart
32	chr19:52801600-52803600	Weak transcription	HSMMtube	muscle
33	chr19:52801600-52803600	Weak transcription	HUVEC	blood vessel
34	chr19:52801600-52803600	Weak transcription	NHLF	lung
35	chr19:52801600-52803800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:52801600-52803800	Weak transcription	Colon Smooth Muscle	Colon
37	chr19:52801600-52803800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr19:52801600-52803800	Weak transcription	Osteobl	bone
39	chr19:52801600-52804000	Weak transcription	HSMM	muscle
40	chr19:52801600-52804000	Weak transcription	NHDF-Ad	bronchial
41	chr19:52801600-52804200	Weak transcription	Brain Angular Gyrus	brain
42	chr19:52801600-52806000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
43	chr19:52801600-52808800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:52801800-52803200	Weak transcription	Brain Germinal Matrix	brain
45	chr19:52801800-52803200	Weak transcription	Colonic Mucosa	Colon
46	chr19:52801800-52803200	Weak transcription	Spleen	Spleen
47	chr19:52801800-52803800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr19:52801800-52804800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
49	chr19:52801800-52805600	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr19:52801800-52827200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links