Variant report

Variant	rs28520081
Chromosome Location	chr19:36979308-36979309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr19:36978905-36981196	SK-N-SH	brain:	n/a	n/a
2	HCFC1	chr19:36979141-36981381	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr19:36979247-36981270	IMR90	lung:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36969427..36971707-chr19:36977964..36979970,2	MCF-7	breast:
2	chr19:36704032..36706423-chr19:36978429..36980490,2	MCF-7	breast:
3	chr19:36979193..36981748-chr19:37061672..37065426,4	K562	blood:
4	chr19:36979208..36981780-chr19:37261367..37264210,2	K562	blood:
5	chr19:36704170..36706461-chr19:36978975..36980989,3	K562	blood:
6	chr19:36977340..36979938-chr19:37058785..37061352,2	K562	blood:
7	chr19:36977221..36979834-chr19:36983552..36985787,2	K562	blood:
8	chr19:36706883..36709067-chr19:36978381..36980309,2	K562	blood:
9	chr19:36867662..36870599-chr19:36976598..36980024,4	K562	blood:
10	chr19:36979124..36982554-chr19:37017679..37020247,4	MCF-7	breast:
11	chr19:36978237..36981071-chr19:36988174..36990152,2	K562	blood:
12	chr19:36978148..36981795-chr19:37018105..37021194,8	K562	blood:
13	chr19:36978821..36980790-chr19:37017858..37020685,3	K562	blood:
14	chr19:36868112..36870123-chr19:36976598..36979565,2	K562	blood:
15	chr19:36978237..36981428-chr19:36988174..36990245,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267309	TF binding region
ENSG00000267260	Chromatin interaction
ENSG00000196357	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000228629	Chromatin interaction
ENSG00000142065	Chromatin interaction
ENSG00000167635	Chromatin interaction
ENSG00000267041	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000267091	Chromatin interaction
ENSG00000266973	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10402838	0.94[ASN][1000 genomes]
rs10407389	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409422	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10409996	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10411104	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10411232	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10416494	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10417866	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10421461	0.88[EUR][1000 genomes]
rs10421862	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10424565	0.82[AMR][1000 genomes]
rs12977285	0.81[AFR][1000 genomes]
rs2967536	0.85[ASN][1000 genomes]
rs71356003	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71356007	0.90[ASN][1000 genomes]
rs9676533	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9967600	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];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	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv1067364	chr19:36921204-36985874	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36957200-36979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:36957400-36979400	Weak transcription	NH-A	brain
3	chr19:36960400-36979600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:36964000-36979800	Weak transcription	Esophagus	oesophagus
5	chr19:36964200-36979400	Weak transcription	Brain Anterior Caudate	brain
6	chr19:36964200-36979600	Weak transcription	Placenta	Placenta
7	chr19:36964200-36979600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:36964600-36979400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:36964800-36979600	Weak transcription	Fetal Kidney	kidney
10	chr19:36966400-36979600	Weak transcription	HSMMtube	muscle
11	chr19:36966600-36979400	Weak transcription	Right Ventricle	heart
12	chr19:36967800-36979600	Weak transcription	Left Ventricle	heart
13	chr19:36970000-36979600	Weak transcription	Psoas Muscle	Psoas
14	chr19:36970000-36979600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr19:36970800-36979800	Weak transcription	Spleen	Spleen
16	chr19:36973800-36979400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:36974400-36979400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:36974400-36979600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:36975200-36979800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:36975400-36979800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:36975800-36979600	ZNF genes & repeats	A549	lung
22	chr19:36976400-36979600	Weak transcription	Thymus	Thymus
23	chr19:36977000-36979600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr19:36977000-36979800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:36977000-36979800	Weak transcription	Ovary	ovary
26	chr19:36978000-36979400	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr19:36978000-36979600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr19:36978000-36979600	Enhancers	Stomach Smooth Muscle	stomach
29	chr19:36978200-36979400	Enhancers	Brain Hippocampus Middle	brain
30	chr19:36978200-36979400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr19:36978200-36979600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:36978200-36979600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr19:36978200-36979600	Enhancers	Brain Angular Gyrus	brain
34	chr19:36978400-36979400	Enhancers	Primary T cells from cord blood	blood
35	chr19:36978400-36979400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:36978400-36981400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:36978800-36979600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr19:36978800-36979600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:36978800-36979800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:36978800-36981000	Active TSS	K562	blood
41	chr19:36979000-36979400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:36979000-36979400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:36979000-36979400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:36979000-36979400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr19:36979000-36979400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr19:36979000-36979400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:36979000-36979400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:36979000-36979400	Enhancers	Fetal Intestine Large	intestine
49	chr19:36979000-36979400	Enhancers	Right Atrium	heart
50	chr19:36979000-36979400	Flanking Active TSS	Hela-S3	cervix

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