Variant report

Variant	rs4653464
Chromosome Location	chr1:226901666-226901667
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	chr1:226889377..226893057-chr1:226895503..226902234,11	MCF-7	breast:
2	chr1:226889403..226893513-chr1:226896039..226901883,9	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1124377	0.83[AMR][1000 genomes]
rs12072939	0.80[AMR][1000 genomes]
rs12095028	0.82[ASN][1000 genomes]
rs16846351	0.88[CHB][hapmap];1.00[AFR][1000 genomes]
rs16846357	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16846378	0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16846413	1.00[AFR][1000 genomes]
rs16846452	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16846458	0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16846461	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16846464	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16846466	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3754398	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754399	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754400	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754401	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754402	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754403	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754406	0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754407	0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754413	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754417	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3768388	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768389	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768397	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768400	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768416	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3820641	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3820647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4653461	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs4653763	1.00[AFR][1000 genomes]
rs4653769	1.00[JPT][hapmap]
rs56095953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58091460	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59173465	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs60932168	1.00[AFR][1000 genomes]
rs7524854	0.88[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	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226891600-226910200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:226891800-226903000	Enhancers	Brain Cingulate Gyrus	brain
3	chr1:226891800-226924800	Weak transcription	Aorta	Aorta
4	chr1:226893400-226918800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:226894400-226902000	Enhancers	Brain Angular Gyrus	brain
6	chr1:226894800-226902400	Weak transcription	Psoas Muscle	Psoas
7	chr1:226895800-226901800	Enhancers	Brain Anterior Caudate	brain
8	chr1:226896000-226901800	Enhancers	Placenta	Placenta
9	chr1:226896000-226902600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:226896000-226903400	Enhancers	Brain Hippocampus Middle	brain
11	chr1:226896200-226901800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:226896200-226909800	Weak transcription	Fetal Intestine Large	intestine
13	chr1:226896600-226910600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:226896800-226901800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:226897000-226901800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:226897000-226901800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:226897000-226910200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:226897200-226902000	Weak transcription	Fetal Intestine Small	intestine
19	chr1:226897200-226905000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:226897400-226902000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:226897400-226905000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:226897600-226902600	Enhancers	Spleen	Spleen
23	chr1:226897600-226904200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:226897600-226905400	Weak transcription	NHLF	lung
25	chr1:226897800-226902000	Enhancers	Brain Substantia Nigra	brain
26	chr1:226898200-226902000	Enhancers	Right Atrium	heart
27	chr1:226899200-226904800	Weak transcription	Stomach Mucosa	stomach
28	chr1:226899200-226911000	Weak transcription	Fetal Lung	lung
29	chr1:226899400-226910000	Weak transcription	Gastric	stomach
30	chr1:226899600-226901800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:226899600-226901800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr1:226899600-226911800	Weak transcription	Small Intestine	intestine
33	chr1:226900200-226902200	Strong transcription	Fetal Stomach	stomach
34	chr1:226900200-226904600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:226900400-226901800	Genic enhancers	Stomach Smooth Muscle	stomach
36	chr1:226900400-226902000	Enhancers	Rectal Smooth Muscle	rectum
37	chr1:226900400-226902200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:226900600-226902000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:226900600-226910200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:226900800-226901800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr1:226900800-226901800	Weak transcription	Right Ventricle	heart
42	chr1:226900800-226901800	Genic enhancers	Thymus	Thymus
43	chr1:226900800-226902000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:226900800-226902800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:226900800-226907000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr1:226900800-226907400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:226900800-226907400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:226900800-226907800	Weak transcription	Pancreas	Pancrea
49	chr1:226900800-226909000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:226900800-226909600	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links