Variant report

Variant	rs27553
Chromosome Location	chr5:16672432-16672433
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	chr5:16670338..16672249-chr5:16672358..16674195,2	MCF-7	breast:
2	chr1:9356327..9359278-chr5:16672338..16674681,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10060275	0.85[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10060411	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11738070	0.88[ASN][1000 genomes]
rs11740825	0.87[JPT][hapmap]
rs1560087	0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1560088	0.88[ASN][1000 genomes]
rs2288432	0.84[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2288433	0.93[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2288434	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2288435	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2288436	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2288437	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2303703	0.93[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2401987	0.93[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs256935	0.84[JPT][hapmap]
rs26745	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26746	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26748	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26749	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs26750	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26757	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26758	0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap];0.91[ASN][1000 genomes]
rs27350	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27501	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs27880	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28056	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs399833	0.84[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap];0.91[ASN][1000 genomes]
rs6881621	0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6889243	0.90[ASN][1000 genomes]
rs7735007	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs890911	0.88[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	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv522062	chr5:16670618-16679966	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16658800-16672600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:16661600-16689400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:16661800-16700000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:16663000-16674800	Weak transcription	Aorta	Aorta
5	chr5:16663000-16712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:16663200-16673000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:16663400-16676600	Strong transcription	A549	lung
8	chr5:16663600-16695400	Strong transcription	Fetal Intestine Small	intestine
9	chr5:16663800-16676600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr5:16663800-16690800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:16663800-16694400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:16663800-16698000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:16663800-16702400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:16663800-16713400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:16664000-16676800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:16664000-16701000	Strong transcription	Fetal Intestine Large	intestine
17	chr5:16664000-16702000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:16664000-16702200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:16664000-16702400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:16664200-16702200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:16664600-16690600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr5:16664800-16674600	Weak transcription	Small Intestine	intestine
23	chr5:16664800-16677600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr5:16665600-16676800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:16665600-16699200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:16666200-16676800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:16666200-16680600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:16667200-16674800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:16667400-16683600	Weak transcription	Liver	Liver
30	chr5:16667600-16673800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:16667600-16676600	Strong transcription	HSMMtube	muscle
32	chr5:16667800-16673400	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr5:16667800-16674800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:16667800-16674800	Weak transcription	Stomach Mucosa	stomach
35	chr5:16667800-16675000	Weak transcription	Left Ventricle	heart
36	chr5:16667800-16676400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:16667800-16677400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr5:16667800-16680000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:16667800-16701000	Weak transcription	Right Ventricle	heart
40	chr5:16668000-16673400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:16668000-16676000	Strong transcription	Brain Hippocampus Middle	brain
42	chr5:16668200-16676400	Strong transcription	Placenta	Placenta
43	chr5:16668600-16672800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:16669200-16672800	Weak transcription	Fetal Thymus	thymus
45	chr5:16669800-16676200	Strong transcription	HSMM	muscle
46	chr5:16670000-16674200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:16670200-16673800	Strong transcription	Brain Substantia Nigra	brain
48	chr5:16670200-16674000	Strong transcription	HMEC	breast
49	chr5:16670200-16676400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:16670200-16676800	Strong transcription	Fetal Muscle Leg	muscle

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