Variant report

Variant	rs73040439
Chromosome Location	chr2:189283028-189283029
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	chr2:189281923..189283556-chr2:189285039..189287990,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10168173	1.00[EUR][1000 genomes]
rs10497688	1.00[EUR][1000 genomes]
rs11678294	0.88[AFR][1000 genomes]
rs11683340	0.88[AFR][1000 genomes]
rs13393870	1.00[EUR][1000 genomes]
rs13394334	1.00[EUR][1000 genomes]
rs13430185	1.00[EUR][1000 genomes]
rs13430412	1.00[EUR][1000 genomes]
rs16829915	1.00[EUR][1000 genomes]
rs16829922	1.00[EUR][1000 genomes]
rs58715158	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58718952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59058494	1.00[EUR][1000 genomes]
rs59329932	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60885306	1.00[EUR][1000 genomes]
rs6705443	1.00[EUR][1000 genomes]
rs6709650	1.00[EUR][1000 genomes]
rs6716922	1.00[EUR][1000 genomes]
rs6721812	1.00[EUR][1000 genomes]
rs73036471	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73036479	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73036496	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040411	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040428	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73040442	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040454	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73041636	1.00[EUR][1000 genomes]
rs73041644	1.00[EUR][1000 genomes]
rs73041648	1.00[EUR][1000 genomes]
rs73041649	1.00[EUR][1000 genomes]
rs7340152	1.00[EUR][1000 genomes]
rs7560857	1.00[EUR][1000 genomes]
rs7577096	1.00[EUR][1000 genomes]
rs7577467	1.00[EUR][1000 genomes]
rs7586703	1.00[EUR][1000 genomes]
rs7588114	1.00[EUR][1000 genomes]
rs7592433	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7592539	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7596417	1.00[EUR][1000 genomes]
rs7597930	1.00[EUR][1000 genomes]
rs7598380	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7599101	1.00[EUR][1000 genomes]
rs9653310	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv533786	chr2:189248503-189354495	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 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	chr2:189251000-189285200	Weak transcription	Aorta	Aorta
2	chr2:189264000-189283800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:189270600-189285200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:189270600-189285200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:189271000-189285200	Weak transcription	Fetal Lung	lung
6	chr2:189276200-189284400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:189276200-189285200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:189276400-189289800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:189276600-189290800	Weak transcription	Placenta	Placenta
10	chr2:189277000-189289400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:189277000-189289600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:189277200-189283600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:189277200-189285200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:189277400-189283600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:189277600-189285200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:189280200-189285200	Weak transcription	Fetal Intestine Large	intestine
17	chr2:189282200-189283400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:189282600-189283400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:189282600-189285000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:189283000-189283400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:189283000-189283400	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links