Variant report

Variant	rs1363959
Chromosome Location	chr5:52071371-52071372
allele	G/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: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1363958	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1363960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363961	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880238	1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs16880266	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs17209816	1.00[CEU][hapmap]
rs1833883	0.98[ASN][1000 genomes]
rs1833884	0.96[ASN][1000 genomes]
rs193438	0.92[ASN][1000 genomes]
rs2133476	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2173525	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs244485	0.92[ASN][1000 genomes]
rs244488	0.87[ASN][1000 genomes]
rs2548503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548506	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548507	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2648732	0.95[ASN][1000 genomes]
rs2648733	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2648734	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2648735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2648737	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs3096173	0.85[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:21 , 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	chr5:52070200-52071600	Weak transcription	Small Intestine	intestine
6	chr5:52070200-52071800	Weak transcription	Right Atrium	heart
7	chr5:52070200-52072000	Weak transcription	Adipose Nuclei	Adipose
8	chr5:52070400-52071400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:52070400-52071400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:52070400-52071600	Weak transcription	Lung	lung
11	chr5:52070400-52071600	Weak transcription	Dnd41	blood
12	chr5:52070400-52071800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:52070400-52071800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:52070600-52071600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr5:52070600-52071600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:52070800-52071800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:52070800-52071800	Weak transcription	Fetal Thymus	thymus
18	chr5:52071200-52073000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:52071200-52073000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr5:52071200-52073000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr5:52071200-52073200	Enhancers	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links