Variant report

Variant	rs5762907
Chromosome Location	chr22:29339085-29339086
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29278303..29280288-chr22:29337849..29340109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12627758	0.92[JPT][hapmap]
rs16986814	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs16986873	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2881637	0.87[EUR][1000 genomes]
rs4823000	0.92[JPT][hapmap]
rs5752820	0.84[AMR][1000 genomes]
rs5752830	0.83[EUR][1000 genomes]
rs5752839	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752851	0.92[JPT][hapmap]
rs5762890	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762891	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762893	0.82[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762895	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762900	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762906	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762919	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs725281	0.93[JPT][hapmap]
rs7286026	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7288513	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7290364	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73388860	0.87[EUR][1000 genomes]
rs8137589	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8140640	0.92[JPT][hapmap]
rs9306461	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs9625621	0.87[EUR][1000 genomes]
rs9625622	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9625628	0.87[EUR][1000 genomes]
rs9625640	0.87[EUR][1000 genomes]
rs9625641	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9625645	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625647	0.85[ASN][1000 genomes]
rs9625657	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs974369	0.84[ASN][1000 genomes]
rs974370	0.81[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29314400-29342800	Weak transcription	Brain Substantia Nigra	brain
2	chr22:29321000-29339600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr22:29331400-29339200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr22:29331400-29339400	Weak transcription	Right Atrium	heart
5	chr22:29331400-29341000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:29331600-29339200	Weak transcription	Pancreas	Pancrea
7	chr22:29331600-29339200	Weak transcription	Psoas Muscle	Psoas
8	chr22:29332000-29343000	Weak transcription	Brain Angular Gyrus	brain
9	chr22:29332600-29339600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr22:29332600-29347600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr22:29333800-29339200	Weak transcription	Lung	lung
12	chr22:29333800-29347800	Weak transcription	Gastric	stomach
13	chr22:29334400-29340400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr22:29334600-29342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr22:29334800-29340000	Enhancers	HepG2	liver
16	chr22:29335000-29339400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:29335400-29339400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr22:29335400-29340000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr22:29335400-29340000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr22:29335800-29347800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr22:29336000-29339800	Enhancers	Fetal Intestine Large	intestine
22	chr22:29336000-29339800	Enhancers	Fetal Intestine Small	intestine
23	chr22:29336200-29347600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr22:29336800-29339400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:29337000-29342000	Weak transcription	A549	lung
26	chr22:29337800-29339800	Enhancers	Duodenum Mucosa	Duodenum
27	chr22:29337800-29340000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr22:29337800-29340400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr22:29338000-29339600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:29338000-29339800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr22:29338000-29339800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr22:29338200-29339400	Enhancers	Fetal Heart	heart
33	chr22:29338200-29339800	Enhancers	Brain Hippocampus Middle	brain
34	chr22:29338200-29339800	Enhancers	Placenta	Placenta
35	chr22:29338200-29340000	Enhancers	Fetal Kidney	kidney
36	chr22:29338200-29340200	Enhancers	Liver	Liver
37	chr22:29338200-29340200	Enhancers	Brain Anterior Caudate	brain
38	chr22:29338400-29339400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr22:29338400-29339600	Enhancers	Small Intestine	intestine
40	chr22:29338400-29340000	Enhancers	Colon Smooth Muscle	Colon
41	chr22:29338600-29339600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr22:29338600-29339800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr22:29338600-29339800	Enhancers	Stomach Mucosa	stomach
44	chr22:29338600-29347600	Weak transcription	Left Ventricle	heart
45	chr22:29338800-29339200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr22:29338800-29339400	Weak transcription	Aorta	Aorta
47	chr22:29338800-29339800	Enhancers	Brain Germinal Matrix	brain
48	chr22:29338800-29339800	Enhancers	Fetal Lung	lung
49	chr22:29338800-29340000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr22:29338800-29340200	Enhancers	Primary monocytes fromperipheralblood	blood

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