Variant report

Variant	rs6844959
Chromosome Location	chr4:173573390-173573391
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:173565287..173567628-chr4:173572131..173574267,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10000607	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10012267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs10022095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10025284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10029310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10031191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10033472	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10034894	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10213357	1.00[JPT][hapmap]
rs10520238	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1097574	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11132960	1.00[JPT][hapmap]
rs11734921	1.00[JPT][hapmap]
rs12108242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12108422	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12512892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12645987	1.00[JPT][hapmap]
rs1370576	1.00[JPT][hapmap]
rs1370577	1.00[JPT][hapmap]
rs1455119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1540474	1.00[JPT][hapmap]
rs1561307	1.00[JPT][hapmap]
rs1658515	1.00[JPT][hapmap]
rs17058675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17058762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17058765	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17058894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17058922	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17058946	1.00[CEU][hapmap]
rs17235632	1.00[JPT][hapmap]
rs1821862	1.00[JPT][hapmap]
rs1870436	1.00[CEU][hapmap]
rs2009141	1.00[CEU][hapmap]
rs2083136	1.00[JPT][hapmap]
rs2118443	1.00[JPT][hapmap]
rs2164822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2164823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2164824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2164826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2332544	1.00[JPT][hapmap]
rs28459425	0.87[EUR][1000 genomes]
rs28484578	0.87[EUR][1000 genomes]
rs28490202	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28529352	0.87[EUR][1000 genomes]
rs28621838	0.87[EUR][1000 genomes]
rs28681326	0.87[EUR][1000 genomes]
rs35345571	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4100737	1.00[JPT][hapmap]
rs4423855	1.00[JPT][hapmap]
rs4572851	1.00[JPT][hapmap]
rs6553647	1.00[JPT][hapmap]
rs6811397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6826006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6827725	1.00[CEU][hapmap]
rs6839897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6841156	1.00[JPT][hapmap]
rs6843452	0.87[EUR][1000 genomes]
rs6848466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs716647	1.00[JPT][hapmap]
rs7671554	1.00[CEU][hapmap]
rs7674050	1.00[JPT][hapmap]
rs7686162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7694652	0.87[EUR][1000 genomes]
rs7694956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7696720	0.87[EUR][1000 genomes]
rs7699455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs837189	1.00[JPT][hapmap]
rs837209	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs837213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9312528	1.00[JPT][hapmap]
rs9312533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9884494	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9884518	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9992243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9992743	0.87[EUR][1000 genomes]
rs9993208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9994145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9995075	1.00[JPT][hapmap]

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	nsv1031592	chr4:173112542-173662991	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537359	chr4:173112542-173662991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534293	chr4:173121379-173606082	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv880685	chr4:173562564-173661711	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv880613	chr4:173569281-173661711	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173571600-173573400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr4:173571600-173573800	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr4:173572400-173573600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr4:173572600-173573600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:173572600-173574200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr4:173572800-173574000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr4:173572800-173574200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:173573000-173574000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:173573000-173574200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr4:173573000-173574200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:173573000-173574200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr4:173573000-173577200	Weak transcription	Fetal Intestine Large	intestine
13	chr4:173573200-173573600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr4:173573200-173574400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr4:173573200-173577200	Weak transcription	Fetal Intestine Small	intestine

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