Variant report

Variant	rs2496420
Chromosome Location	chr13:39256838-39256839
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:39251230..39253233-chr13:39256150..39258363,2	MCF-7	breast:
2	chr13:39255037..39256959-chr13:39258816..39261083,2	MCF-7	breast:
3	chr13:39256386..39258055-chr13:39258985..39261054,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11147723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11147724	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11147725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244358	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2053848	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122208	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122212	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2197879	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442335	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442339	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442340	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442341	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442343	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442344	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2442373	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442379	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496418	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496419	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496425	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2496433	0.80[ASN][1000 genomes]
rs35378642	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4329795	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55860060	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55880170	0.80[ASN][1000 genomes]
rs55922882	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563629	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331440	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7991701	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs895895	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs930659	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs930660	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9566354	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9576589	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576590	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576591	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576592	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576595	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634754	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9788341	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39253200-39259000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr13:39254400-39259000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr13:39254400-39259600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:39254400-39259600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr13:39254400-39259600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr13:39255200-39259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:39255200-39260200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr13:39255400-39259600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:39255800-39259400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:39255800-39260200	Weak transcription	Adipose Nuclei	Adipose
11	chr13:39256000-39257600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:39256000-39259000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:39256200-39259000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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