Variant report

Variant	rs3768416
Chromosome Location	chr1:226921440-226921441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDC42BPA-5	chr1:226920314-226922612	NONHSAT009902

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]
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]
rs4653464	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:104 , 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	chr1:226910200-226922400	Weak transcription	Fetal Brain Male	brain
5	chr1:226912000-226923200	Weak transcription	NH-A	brain
6	chr1:226912200-226921800	Weak transcription	NHDF-Ad	bronchial
7	chr1:226912200-226922000	Weak transcription	HMEC	breast
8	chr1:226912200-226923600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:226912400-226924600	Weak transcription	Ovary	ovary
10	chr1:226912800-226921800	Weak transcription	Placenta	Placenta
11	chr1:226912800-226925400	Weak transcription	Stomach Mucosa	stomach
12	chr1:226913600-226923000	Weak transcription	Gastric	stomach
13	chr1:226915000-226925000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
14	chr1:226916600-226923400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:226916800-226924200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:226918400-226921800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:226918600-226925000	Transcr. at gene 5' and 3'	Thymus	Thymus
18	chr1:226918800-226922400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:226918800-226925000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
20	chr1:226918800-226925800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:226919200-226924400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:226919400-226924000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:226919600-226923200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:226920000-226925200	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:226920200-226924000	Genic enhancers	Primary hematopoietic stem cells	blood
26	chr1:226920400-226921600	Flanking Active TSS	Brain Substantia Nigra	brain
27	chr1:226920400-226921800	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:226920400-226921800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr1:226920400-226922000	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr1:226920400-226922000	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr1:226920400-226922000	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr1:226920400-226923400	Strong transcription	Fetal Intestine Large	intestine
33	chr1:226920400-226923600	Enhancers	Small Intestine	intestine
34	chr1:226920400-226924200	Transcr. at gene 5' and 3'	Dnd41	blood
35	chr1:226920400-226924400	Genic enhancers	Spleen	Spleen
36	chr1:226920400-226924600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:226920400-226924600	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:226920400-226924600	Genic enhancers	Fetal Lung	lung
39	chr1:226920400-226924800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
40	chr1:226920400-226924800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
41	chr1:226920400-226925000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
42	chr1:226920400-226927000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
43	chr1:226920600-226921800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:226920600-226922000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:226920600-226922400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:226920600-226923400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:226920600-226923600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
48	chr1:226920600-226923800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
49	chr1:226920600-226924400	Genic enhancers	Primary monocytes fromperipheralblood	blood
50	chr1:226920600-226924600	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose

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