Variant report

Variant	rs1404770
Chromosome Location	chr2:47424262-47424263
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47412361..47428396-chr2:47486545..47501626,43	MCF-7	breast:
2	chr2:47194544..47196937-chr2:47423756..47426631,2	MCF-7	breast:
3	chr2:47423169..47425083-chr2:47433358..47436246,2	K562	blood:
4	chr2:47422552..47429870-chr2:47496148..47502457,12	MCF-7	breast:
5	chr2:47421460..47424746-chr2:47425269..47428028,4	K562	blood:

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

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

rs_ID	r²[population]
rs11125126	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12991318	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1630239	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1693863	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1693864	0.88[ASN][1000 genomes]
rs1693882	0.84[ASN][1000 genomes]
rs1723482	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs1723484	0.91[CHB][hapmap]
rs1995108	0.97[ASN][1000 genomes]
rs2036162	0.86[AFR][1000 genomes]
rs2454082	0.84[ASN][1000 genomes]
rs2454083	0.84[ASN][1000 genomes]
rs2462588	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2462589	0.97[ASN][1000 genomes]
rs6713934	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6751198	0.93[ASN][1000 genomes]
rs7581908	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7606478	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs815802	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs815809	0.86[YRI][hapmap]
rs815815	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs815816	0.90[CHB][hapmap]
rs815817	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878665	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47419800-47424800	Enhancers	NH-A	brain
2	chr2:47419800-47425200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:47419800-47426000	Weak transcription	Pancreas	Pancrea
4	chr2:47420200-47426400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:47420600-47428000	Weak transcription	Ovary	ovary
6	chr2:47421200-47424400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr2:47421400-47424600	Weak transcription	Fetal Thymus	thymus
8	chr2:47421400-47426200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:47421400-47428200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:47421400-47432200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:47421400-47432800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:47421600-47426200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:47421600-47432600	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:47422200-47426000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:47422200-47426000	Weak transcription	Lung	lung
16	chr2:47422200-47426200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:47422200-47432800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:47422400-47425600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:47422400-47425800	Weak transcription	K562	blood
20	chr2:47422400-47426000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:47422400-47426000	Weak transcription	Placenta	Placenta
22	chr2:47422400-47427200	Enhancers	A549	lung
23	chr2:47422400-47428000	Weak transcription	Brain Anterior Caudate	brain
24	chr2:47422400-47428000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:47422400-47428200	Weak transcription	Brain Angular Gyrus	brain
26	chr2:47422600-47425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:47422600-47425800	Weak transcription	NHEK	skin
28	chr2:47422600-47426000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:47422600-47426000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:47422600-47426000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:47422600-47426000	Weak transcription	NHDF-Ad	bronchial
32	chr2:47422600-47426000	Weak transcription	NHLF	lung
33	chr2:47422600-47427200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:47422600-47427800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:47423000-47426000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:47423200-47425400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:47423200-47432400	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:47423400-47424600	Weak transcription	HSMM	muscle
39	chr2:47423400-47425400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:47423400-47425600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:47423400-47425600	Weak transcription	Osteobl	bone
42	chr2:47423400-47425800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:47423400-47426000	Weak transcription	Hela-S3	cervix
44	chr2:47423600-47426000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:47423800-47424600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:47423800-47425000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:47423800-47428000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:47423800-47431400	Weak transcription	Brain Substantia Nigra	brain
49	chr2:47424000-47425000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:47424000-47425200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links