Variant report

Variant	rs2552290
Chromosome Location	chr6:5473488-5473489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5471400..5474244-chr6:6052015..6054966,2	MCF-7	breast:
2	chr6:5473023..5474708-chr6:5475378..5477106,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs68099711	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72817727	0.80[AMR][1000 genomes]
rs73354473	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9392687	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9405270	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv600886	chr6:5426265-5511614	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5434200-5487000	Weak transcription	Aorta	Aorta
2	chr6:5449000-5499400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:5456400-5486000	Weak transcription	Thymus	Thymus
4	chr6:5457400-5481200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:5457800-5487400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:5458800-5483000	Weak transcription	Pancreas	Pancrea
7	chr6:5459000-5486400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:5461600-5507200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:5466400-5518200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr6:5466600-5506400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:5466800-5502200	Weak transcription	Gastric	stomach
12	chr6:5467200-5477000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:5467200-5477600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:5467200-5487400	Weak transcription	Lung	lung
15	chr6:5468400-5487800	Weak transcription	Primary B cells from cord blood	blood
16	chr6:5469800-5481200	Weak transcription	Esophagus	oesophagus
17	chr6:5471000-5473600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:5471200-5474400	Weak transcription	K562	blood
19	chr6:5471400-5474400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:5471400-5481000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:5471600-5473600	Enhancers	Fetal Brain Male	brain
22	chr6:5471600-5487400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:5471800-5489400	Weak transcription	Small Intestine	intestine
24	chr6:5471800-5505800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:5472200-5481200	Weak transcription	Primary T cells from cord blood	blood
26	chr6:5472200-5481200	Weak transcription	Left Ventricle	heart
27	chr6:5472200-5487400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr6:5472400-5474000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr6:5472400-5511600	Weak transcription	Fetal Stomach	stomach
30	chr6:5472600-5474400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:5472600-5491800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:5472600-5496800	Weak transcription	NHDF-Ad	bronchial
33	chr6:5472600-5499400	Weak transcription	Spleen	Spleen
34	chr6:5472600-5501800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:5472600-5506200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:5472800-5474000	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr6:5472800-5474200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:5473000-5473800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:5473200-5477200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:5473200-5481000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:5473400-5474200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links