Variant report

Variant	rs56095953
Chromosome Location	chr1:226923396-226923397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1124377	0.83[AMR][1000 genomes]
rs12072939	0.80[AMR][1000 genomes]
rs12095028	0.82[ASN][1000 genomes]
rs16846351	1.00[AFR][1000 genomes]
rs16846357	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16846378	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	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	0.86[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	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754407	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754413	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3820641	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3820647	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4653461	0.82[ASN][1000 genomes]
rs4653464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4653763	1.00[AFR][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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226891800-226924800	Weak transcription	Aorta	Aorta
2	chr1:226909800-226924200	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr1:226910000-226925000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
4	chr1:226912200-226923600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:226912400-226924600	Weak transcription	Ovary	ovary
6	chr1:226912800-226925400	Weak transcription	Stomach Mucosa	stomach
7	chr1:226915000-226925000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
8	chr1:226916600-226923400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:226916800-226924200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:226918600-226925000	Transcr. at gene 5' and 3'	Thymus	Thymus
11	chr1:226918800-226925000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
12	chr1:226918800-226925800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:226919200-226924400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:226919400-226924000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:226920000-226925200	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:226920200-226924000	Genic enhancers	Primary hematopoietic stem cells	blood
17	chr1:226920400-226923400	Strong transcription	Fetal Intestine Large	intestine
18	chr1:226920400-226923600	Enhancers	Small Intestine	intestine
19	chr1:226920400-226924200	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr1:226920400-226924400	Genic enhancers	Spleen	Spleen
21	chr1:226920400-226924600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:226920400-226924600	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:226920400-226924600	Genic enhancers	Fetal Lung	lung
24	chr1:226920400-226924800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
25	chr1:226920400-226924800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
26	chr1:226920400-226925000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
27	chr1:226920400-226927000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
28	chr1:226920600-226923400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:226920600-226923600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
30	chr1:226920600-226923800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
31	chr1:226920600-226924400	Genic enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:226920600-226924600	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
33	chr1:226920600-226924800	Strong transcription	NHEK	skin
34	chr1:226920600-226925000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:226920600-226925000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:226920600-226925000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
37	chr1:226920800-226923400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:226920800-226923400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:226920800-226927200	Active TSS	Psoas Muscle	Psoas
40	chr1:226921000-226923600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:226921000-226924000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:226921000-226924800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:226921000-226927600	Active TSS	Right Atrium	heart
44	chr1:226921200-226923800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:226921200-226924800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:226921600-226923400	Genic enhancers	HUVEC	blood vessel
47	chr1:226921600-226923600	Transcr. at gene 5' and 3'	Left Ventricle	heart
48	chr1:226921600-226924600	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
49	chr1:226921600-226924600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
50	chr1:226921800-226923800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach

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