Variant report

Variant	rs61839590
Chromosome Location	chr1:223002304-223002305
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:223002220-223002370	HAc	cerebellar:	n/a	n/a
2	MYC	chr1:223002157-223002492	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr1:223002287-223002568	MCF-7	breast:	n/a	chr1:223002475-223002493 chr1:223002470-223002491
4	CTCF	chr1:223002300-223002450	AG04450	lung:	n/a	n/a
5	BRCA1	chr1:223002283-223002612	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr1:223002260-223002410	HCT-116	colon:	n/a	n/a
7	CTCF	chr1:223002300-223002450	HCM	heart:	n/a	n/a
8	CTCF	chr1:223002220-223002370	HFF	foreskin:	n/a	n/a
9	SMC3	chr1:223002289-223002578	Hela-S3	cervix:	n/a	chr1:223002477-223002491
10	CTCF	chr1:223002080-223002350	HCT-116	colon:	n/a	n/a
11	CTCF	chr1:223002280-223002430	BE2_C	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:222998480..223000211-chr1:223000918..223003363,2	MCF-7	breast:
2	chr1:222986827..222988630-chr1:223000881..223002859,2	MCF-7	breast:
3	chr1:223001258..223003363-chr1:223007467..223009599,2	MCF-7	breast:
4	chr1:222968648..222969417-chr1:223001961..223002499,2	MCF-7	breast:
5	chr1:222986729..222989819-chr1:223001002..223005734,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228106	TF binding region
ENSG00000228106	Chromatin interaction
ENSG00000154309	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11487817	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11487861	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11597	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17163510	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17163518	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17163525	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35271605	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35530937	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35980718	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4415571	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61838109	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61839585	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61839593	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61839607	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61839609	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61839610	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61839658	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61839659	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61840262	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61840269	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61840288	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61840295	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9441849	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9441937	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222989400-223002800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:222989400-223026800	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:222990400-223027400	Weak transcription	Primary B cells from cord blood	blood
4	chr1:222991200-223010200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:222991800-223003200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:222991800-223017200	Weak transcription	Aorta	Aorta
7	chr1:222994000-223003200	Weak transcription	Osteobl	bone
8	chr1:222994600-223003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:222994800-223003200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:222995000-223002600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:222995200-223003400	Weak transcription	NHDF-Ad	bronchial
12	chr1:222995800-223003200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:222997000-223016600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:222998200-223003200	Weak transcription	A549	lung
15	chr1:222998200-223003600	Weak transcription	Ovary	ovary
16	chr1:222998400-223002400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:222998400-223006600	Weak transcription	Fetal Lung	lung
18	chr1:222998600-223003400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:222999400-223003200	Weak transcription	Stomach Mucosa	stomach
20	chr1:222999600-223002600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:222999600-223002600	Weak transcription	HepG2	liver
22	chr1:222999600-223002800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:222999600-223015600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:223001200-223002400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:223001200-223002400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:223001200-223002800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr1:223001200-223003400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:223001400-223002600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:223001400-223003400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr1:223001600-223002400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:223001600-223002600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:223001800-223003800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:223001800-223004000	Enhancers	Colon Smooth Muscle	Colon
34	chr1:223001800-223012000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:223001800-223012200	Weak transcription	Hela-S3	cervix
36	chr1:223002000-223002400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:223002000-223002800	Weak transcription	Brain Substantia Nigra	brain
38	chr1:223002200-223017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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