Variant report

Variant	rs72949137
Chromosome Location	chr2:58251573-58251574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:58249060..58252224-chr2:58272620..58275638,4	MCF-7	breast:
2	chr2:58250269..58252783-chr2:58272137..58273810,2	K562	blood:
3	chr2:58250871..58252381-chr2:58256903..58259495,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10164499	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10165760	0.92[AFR][1000 genomes]
rs10174202	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10176681	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10178025	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10182762	0.88[AFR][1000 genomes]
rs10187411	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10191766	0.87[AMR][1000 genomes]
rs10201793	0.87[AMR][1000 genomes]
rs10203014	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1025755	0.89[AFR][1000 genomes]
rs10518852	0.87[AMR][1000 genomes]
rs11883874	0.92[AFR][1000 genomes]
rs11891477	0.88[AFR][1000 genomes]
rs11892302	0.89[AFR][1000 genomes]
rs13382369	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13394820	0.94[AFR][1000 genomes]
rs13400997	0.87[AMR][1000 genomes]
rs13405281	0.92[AFR][1000 genomes]
rs13410500	0.92[AFR][1000 genomes]
rs13419989	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13431271	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2165100	0.92[AFR][1000 genomes]
rs2165103	0.89[AFR][1000 genomes]
rs28521626	0.94[AFR][1000 genomes]
rs4459722	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57112138	0.82[AFR][1000 genomes]
rs57597086	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58470176	0.92[AFR][1000 genomes]
rs6718190	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72949131	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949158	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951042	0.87[AFR][1000 genomes]
rs72951048	0.92[AFR][1000 genomes]
rs72951056	0.92[AFR][1000 genomes]
rs73944804	0.88[AFR][1000 genomes]
rs7563225	0.87[AMR][1000 genomes]
rs7563312	0.85[AFR][1000 genomes]
rs7569731	0.86[AFR][1000 genomes]
rs7574578	0.87[AMR][1000 genomes]
rs7574694	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7600213	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9973345	0.83[AFR][1000 genomes]
rs9973928	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874200	chr2:58163178-58262016	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58249600-58259800	Weak transcription	Ovary	ovary
2	chr2:58250400-58252000	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr2:58250600-58251600	Enhancers	Primary B cells from cord blood	blood
4	chr2:58250600-58251600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr2:58251200-58251600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr2:58251400-58251800	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:58251400-58251800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:58251400-58251800	Flanking Active TSS	GM12878-XiMat	blood
9	chr2:58251400-58272000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links