Variant report

Variant	rs2648732
Chromosome Location	chr5:52072164-52072165
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	chr5:52069827..52072246-chr5:52094290..52096328,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1363958	0.92[ASN][1000 genomes]
rs1363959	0.95[ASN][1000 genomes]
rs1363960	0.95[ASN][1000 genomes]
rs1363961	0.95[ASN][1000 genomes]
rs16880238	0.94[CHB][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16880266	0.93[CHB][hapmap];0.87[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1833883	0.93[ASN][1000 genomes]
rs1833884	0.91[ASN][1000 genomes]
rs193438	0.87[ASN][1000 genomes]
rs2133476	0.90[ASN][1000 genomes]
rs2173525	0.90[ASN][1000 genomes]
rs2245991	0.94[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2245997	1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs244485	0.87[ASN][1000 genomes]
rs244488	0.83[ASN][1000 genomes]
rs2548503	0.95[ASN][1000 genomes]
rs2548504	0.95[ASN][1000 genomes]
rs2548505	0.95[ASN][1000 genomes]
rs2548506	0.95[ASN][1000 genomes]
rs2648733	0.95[ASN][1000 genomes]
rs2648734	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2648735	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2648736	1.00[EUR][1000 genomes]
rs3096173	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1027410	chr5:52022713-52103360	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1024123	chr5:52052104-52089545	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020640	chr5:52058830-52120858	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52066800-52072600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr5:52067000-52073200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:52068000-52073200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr5:52068400-52074000	Enhancers	Primary T cells from cord blood	blood
5	chr5:52071200-52073000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:52071200-52073000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr5:52071200-52073000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:52071200-52073200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr5:52071400-52072600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:52071400-52072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr5:52071600-52072200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr5:52071600-52072200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:52071600-52072200	Enhancers	Lung	lung
14	chr5:52071600-52072200	Enhancers	Small Intestine	intestine
15	chr5:52071600-52072600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:52071600-52072600	Enhancers	Dnd41	blood
17	chr5:52071600-52073000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr5:52071800-52072200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:52071800-52072200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:52071800-52072200	Enhancers	Fetal Thymus	thymus
21	chr5:52071800-52072600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr5:52072000-52072200	Enhancers	GM12878-XiMat	blood
23	chr5:52072000-52072600	Enhancers	Adipose Nuclei	Adipose
24	chr5:52072000-52072600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr5:52072000-52074200	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links