Variant report

Variant	rs5752842
Chromosome Location	chr22:29349899-29349900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29344969..29347183-chr22:29349320..29351089,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12627758	0.92[JPT][hapmap]
rs16986814	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs16986873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4823000	0.92[JPT][hapmap]
rs5752820	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs5752839	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752851	0.92[JPT][hapmap]
rs5762890	0.82[ASN][1000 genomes]
rs5762891	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs5762893	0.82[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs5762895	0.84[ASN][1000 genomes]
rs5762900	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762906	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762907	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]
rs5762919	0.85[CEU][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs725281	0.93[JPT][hapmap]
rs7286026	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7288513	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs7290364	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8137589	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8140640	0.92[JPT][hapmap]
rs9306461	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs9625621	1.00[AFR][1000 genomes]
rs9625622	1.00[CEU][hapmap]
rs9625641	0.82[ASN][1000 genomes]
rs9625645	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs9625647	0.84[ASN][1000 genomes]
rs9625657	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs974369	0.86[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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29339800-29352600	Weak transcription	Stomach Mucosa	stomach
2	chr22:29345200-29350800	Enhancers	Fetal Muscle Leg	muscle
3	chr22:29345400-29350000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr22:29345400-29350000	Enhancers	Fetal Lung	lung
5	chr22:29345600-29350200	Enhancers	Fetal Kidney	kidney
6	chr22:29345800-29350000	Enhancers	Rectal Smooth Muscle	rectum
7	chr22:29345800-29350600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr22:29345800-29351200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr22:29346000-29350000	Enhancers	Liver	Liver
10	chr22:29346400-29353800	Weak transcription	NHEK	skin
11	chr22:29346400-29357400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr22:29346600-29352800	Weak transcription	Brain Substantia Nigra	brain
13	chr22:29347000-29350800	Enhancers	Placenta	Placenta
14	chr22:29347200-29350400	Enhancers	Osteobl	bone
15	chr22:29347400-29350000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr22:29347400-29350400	Enhancers	Fetal Intestine Large	intestine
17	chr22:29347400-29350400	Genic enhancers	Fetal Intestine Small	intestine
18	chr22:29347400-29350400	Enhancers	Ovary	ovary
19	chr22:29347600-29350000	Enhancers	Fetal Stomach	stomach
20	chr22:29347600-29350200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr22:29347600-29350200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr22:29347600-29350400	Enhancers	Psoas Muscle	Psoas
23	chr22:29347600-29356200	Weak transcription	Brain Germinal Matrix	brain
24	chr22:29347800-29350000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr22:29347800-29350400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr22:29348000-29350400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr22:29348000-29350800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr22:29348000-29352400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr22:29348200-29350800	Enhancers	HSMMtube	muscle
30	chr22:29348200-29351400	Enhancers	HepG2	liver
31	chr22:29348200-29351800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr22:29348200-29351800	Weak transcription	Lung	lung
33	chr22:29348200-29352000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr22:29348200-29353800	Enhancers	Colon Smooth Muscle	Colon
35	chr22:29348200-29365000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr22:29348400-29351400	Weak transcription	Spleen	Spleen
37	chr22:29348400-29352400	Weak transcription	Brain Angular Gyrus	brain
38	chr22:29348400-29352600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:29348600-29350000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr22:29348600-29351800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr22:29348800-29350000	Enhancers	Left Ventricle	heart
42	chr22:29348800-29360400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr22:29349000-29352000	Weak transcription	Brain Anterior Caudate	brain
44	chr22:29349200-29350000	Enhancers	Esophagus	oesophagus
45	chr22:29349200-29350200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr22:29349200-29352000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr22:29349200-29352000	Weak transcription	Brain Hippocampus Middle	brain
48	chr22:29349200-29352200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr22:29349200-29352400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr22:29349200-29356800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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