Variant report

Variant	rs10028755
Chromosome Location	chr4:53434501-53434502
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	chr4:53424700..53426749-chr4:53432925..53434502,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10000311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10001085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10001370	0.84[ASN][1000 genomes]
rs10001387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10002261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10010306	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10012676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10014740	1.00[CEU][hapmap]
rs10014752	0.90[ASN][1000 genomes]
rs10014850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10020568	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10021143	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10023867	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];0.90[ASN][1000 genomes]
rs10027906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10028085	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10029145	0.90[ASN][1000 genomes]
rs10031386	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10032700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10033218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10471216	0.90[ASN][1000 genomes]
rs13434726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13435157	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]
rs28376189	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28376284	1.00[AFR][1000 genomes]
rs28379922	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28380682	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28396506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402205	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28411005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28412170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28430452	0.90[ASN][1000 genomes]
rs28436702	0.87[AFR][1000 genomes]
rs28451750	0.90[ASN][1000 genomes]
rs28475600	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28478374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28482298	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28503210	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28514875	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28565016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28588481	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28590396	0.90[ASN][1000 genomes]
rs28619184	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28644292	0.90[ASN][1000 genomes]
rs28651623	1.00[AFR][1000 genomes]
rs28654693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28660550	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28660571	0.90[ASN][1000 genomes]
rs28672279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28694544	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28711292	1.00[AFR][1000 genomes]
rs28721897	0.90[ASN][1000 genomes]
rs28722174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28784684	0.90[ASN][1000 genomes]
rs28825181	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs28825412	0.90[ASN][1000 genomes]
rs28849759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28852068	0.90[ASN][1000 genomes]
rs6830833	0.90[ASN][1000 genomes]
rs7673679	1.00[ASN][1000 genomes]
rs9990686	0.90[ASN][1000 genomes]
rs9994643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9997863	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv999397	chr4:53157525-53448384	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv482581	chr4:53310749-53480710	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1009480	chr4:53338708-53436560	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537092	chr4:53338708-53436560	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53427400-53436200	Weak transcription	Right Ventricle	heart
2	chr4:53427600-53439000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:53427800-53438800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:53432600-53438400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:53433000-53435600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:53433200-53435200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:53433200-53443800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:53433400-53435000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr4:53433400-53435400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:53433400-53436000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:53433800-53435600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:53434000-53435400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr4:53434000-53435400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr4:53434000-53435600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr4:53434000-53441800	Weak transcription	Left Ventricle	heart
16	chr4:53434200-53435200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:53434200-53443000	Weak transcription	Fetal Heart	heart
18	chr4:53434400-53434800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:53434400-53434800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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