Variant report

Variant	rs7689911
Chromosome Location	chr4:100025508-100025509
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	chr4:100009811..100011847-chr4:100024562..100026344,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246090	Chromatin interaction
ENSG00000197894	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs17028473	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17028505	0.89[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17028834	1.00[AMR][1000 genomes]
rs28364319	1.00[AMR][1000 genomes]
rs28730571	1.00[AMR][1000 genomes]
rs28730610	1.00[AMR][1000 genomes]
rs28730644	0.93[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs29001339	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs29001631	1.00[AMR][1000 genomes]
rs55820222	1.00[AMR][1000 genomes]
rs59728850	1.00[AMR][1000 genomes]
rs6532799	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6827292	0.93[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs6828819	1.00[AMR][1000 genomes]
rs6831854	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835771	1.00[AMR][1000 genomes]
rs72897134	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72901271	1.00[AMR][1000 genomes]
rs72901287	1.00[AMR][1000 genomes]
rs72901294	1.00[AMR][1000 genomes]
rs72901295	1.00[AMR][1000 genomes]
rs7664906	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7684674	1.00[AMR][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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr4:100011400-100025800	Weak transcription	Esophagus	oesophagus
2	chr4:100011600-100025600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
4	chr4:100020600-100034800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:100020800-100032800	Weak transcription	Fetal Intestine Small	intestine
6	chr4:100020800-100038600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:100021000-100032200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:100021000-100041200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:100023800-100025800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:100024000-100025800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:100024000-100025800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:100024800-100025600	Enhancers	Adipose Nuclei	Adipose
14	chr4:100025000-100025800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:100025400-100025800	Enhancers	Placenta Amnion	Placenta Amnion

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