Variant report

Variant	rs6878896
Chromosome Location	chr5:90205537-90205538
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90205148..90207152-chr5:90211659..90214340,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10035662	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10044202	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10052015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10053303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs10059629	0.92[CHB][hapmap]
rs10060641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10061193	0.81[ASN][1000 genomes]
rs10078496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10078568	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs10079044	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10474336	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10514340	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12054681	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12055217	0.90[ASN][1000 genomes]
rs12513628	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12515473	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12515481	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12520956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12522395	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13353995	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13355731	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16869175	0.83[CHB][hapmap]
rs17556421	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247415	0.92[CHB][hapmap]
rs2366935	0.91[CHB][hapmap]
rs2438338	0.84[CHB][hapmap]
rs2438342	0.84[CHB][hapmap]
rs2438343	0.92[CHB][hapmap]
rs2438344	0.92[CHB][hapmap]
rs2438345	0.83[CHB][hapmap]
rs2438353	0.92[CHB][hapmap]
rs2443068	0.83[CHB][hapmap]
rs28437109	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28597697	0.89[ASN][1000 genomes]
rs3098356	0.83[CHB][hapmap]
rs4916698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[ASN][1000 genomes]
rs4916826	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4916827	0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4916828	0.82[ASN][1000 genomes]
rs4916829	0.83[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55977992	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56908576	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57107124	0.80[EUR][1000 genomes]
rs57954532	0.90[ASN][1000 genomes]
rs58201771	0.90[ASN][1000 genomes]
rs73185149	0.86[ASN][1000 genomes]
rs73185150	0.90[ASN][1000 genomes]
rs7724016	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	esv2754394	chr5:90181320-90225796	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90185000-90226600	Weak transcription	K562	blood
2	chr5:90186400-90218000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:90195800-90207000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:90201200-90205800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:90204400-90205600	Enhancers	HUVEC	blood vessel
6	chr5:90204600-90205600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:90204600-90206200	Enhancers	Liver	Liver
8	chr5:90204600-90208200	Enhancers	HepG2	liver
9	chr5:90204800-90206000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr5:90204800-90206200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:90204800-90206400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr5:90204800-90208800	Enhancers	A549	lung
13	chr5:90205000-90225000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:90205200-90206000	Weak transcription	Fetal Kidney	kidney
15	chr5:90205200-90210200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:90205200-90210600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:90205200-90217600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:90205200-90219200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:90205400-90205800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:90205400-90207800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links