Variant report

Variant	rs3753653
Chromosome Location	chr1:225968809-225968810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:
2	chr1:225966591..225969033-chr1:226010866..226013102,3	MCF-7	breast:
3	chr1:225966963..225971678-chr1:225973611..225976928,7	K562	blood:
4	chr1:225615356..225617168-chr1:225967552..225969284,2	K562	blood:
5	chr1:225966585..225968935-chr1:226308385..226311332,2	MCF-7	breast:
6	chr1:225963461..225967975-chr1:225968057..225975345,14	MCF-7	breast:
7	chr1:225967558..225969741-chr1:225995095..225998302,3	MCF-7	breast:
8	chr1:225968570..225970564-chr1:226082071..226083838,2	K562	blood:
9	chr1:225963904..225970275-chr1:225994893..226001084,15	K562	blood:
10	chr1:225955657..225958331-chr1:225968298..225970381,2	K562	blood:
11	chr1:225964257..225969087-chr1:226030786..226035881,7	K562	blood:
12	chr1:225965000..225971731-chr1:226051573..226055609,6	K562	blood:
13	chr1:225648477..225651119-chr1:225966156..225969061,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143815	Chromatin interaction
ENSG00000242861	Chromatin interaction
ENSG00000143819	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10799325	0.80[ASN][1000 genomes]
rs3753651	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3753654	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58076029	0.88[ASN][1000 genomes]
rs58548524	0.88[ASN][1000 genomes]
rs59409022	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225966200-225969000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr1:225966200-225973400	Weak transcription	Esophagus	oesophagus
3	chr1:225966800-225969800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:225966800-225970400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:225966800-225972600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:225966800-225978600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:225967000-225969000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:225967000-225970400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:225967000-225971800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:225967000-225972200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:225967000-225973600	Weak transcription	HSMMtube	muscle
12	chr1:225967200-225969600	Enhancers	Liver	Liver
13	chr1:225967200-225969800	Weak transcription	Fetal Intestine Large	intestine
14	chr1:225967200-225970000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:225967200-225970200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:225967200-225970600	Weak transcription	HSMM	muscle
17	chr1:225967200-225970800	Enhancers	Adipose Nuclei	Adipose
18	chr1:225967200-225971800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr1:225967200-225972200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:225967200-225972600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:225967200-225978400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:225967400-225969000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:225967400-225969000	Strong transcription	Placenta	Placenta
24	chr1:225967400-225971800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr1:225967400-225971800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:225967600-225970600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr1:225967600-225971000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:225967600-225971200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr1:225967600-225973600	Weak transcription	Fetal Kidney	kidney
30	chr1:225967800-225969000	Genic enhancers	H1 Cell Line	embryonic stem cell
31	chr1:225967800-225969000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:225967800-225969000	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:225967800-225969000	Enhancers	Brain Hippocampus Middle	brain
34	chr1:225967800-225969000	Enhancers	Brain Substantia Nigra	brain
35	chr1:225967800-225969000	Genic enhancers	A549	lung
36	chr1:225967800-225969400	Weak transcription	NHLF	lung
37	chr1:225967800-225969600	Enhancers	Brain Anterior Caudate	brain
38	chr1:225967800-225969800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:225967800-225969800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:225967800-225970200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:225967800-225970600	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr1:225967800-225970600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:225967800-225970800	Genic enhancers	K562	blood
44	chr1:225967800-225971200	Enhancers	Rectal Smooth Muscle	rectum
45	chr1:225967800-225971400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:225967800-225971600	Genic enhancers	Fetal Lung	lung
47	chr1:225967800-225971800	Enhancers	Brain Angular Gyrus	brain
48	chr1:225967800-225980200	Weak transcription	Stomach Mucosa	stomach
49	chr1:225968000-225969000	Enhancers	Stomach Smooth Muscle	stomach
50	chr1:225968000-225969400	Weak transcription	Fetal Heart	heart

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