Variant report

Variant	rs1840229
Chromosome Location	chr4:100026109-100026110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100009811..100011847-chr4:100024562..100026344,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246090	Chromatin interaction
ENSG00000197894	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1133485	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1154400	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1154401	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1154403	0.89[EUR][1000 genomes]
rs1154405	0.83[AMR][1000 genomes]
rs1154406	0.83[AMR][1000 genomes]
rs1154410	0.83[AMR][1000 genomes]
rs12502237	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12506256	0.82[AMR][1000 genomes]
rs13107558	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1311615	0.83[AMR][1000 genomes]
rs1311616	0.83[AMR][1000 genomes]
rs1311617	0.83[AMR][1000 genomes]
rs1311618	0.83[AMR][1000 genomes]
rs1311619	0.83[AMR][1000 genomes]
rs1311620	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1377689	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1453872	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1453873	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1453874	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1840228	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1840230	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1840231	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1901922	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2034696	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602840	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2602841	0.84[EUR][1000 genomes]
rs2602845	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602846	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602847	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602851	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2602853	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2602854	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2602855	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602856	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2602857	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2602858	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602859	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602860	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2602862	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2602865	0.80[AMR][1000 genomes]
rs2602866	0.80[AMR][1000 genomes]
rs2602873	0.80[AMR][1000 genomes]
rs2602875	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2602876	0.82[AMR][1000 genomes]
rs2602877	0.82[AMR][1000 genomes]
rs2602878	0.82[AMR][1000 genomes]
rs2851256	0.80[AMR][1000 genomes]
rs2851257	0.80[AMR][1000 genomes]
rs2851259	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2851260	0.80[AMR][1000 genomes]
rs2851263	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851265	0.83[AMR][1000 genomes]
rs2851266	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851267	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851268	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851269	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851270	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2851274	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2851277	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851278	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851279	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2851283	0.80[AMR][1000 genomes]
rs2851284	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851285	0.81[AMR][1000 genomes]
rs2851286	0.83[AMR][1000 genomes]
rs2924580	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2924585	0.85[AFR][1000 genomes]
rs3018046	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3018047	0.83[AMR][1000 genomes]
rs3018048	0.83[AMR][1000 genomes]
rs3100630	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3133152	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4235435	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4235436	0.80[AMR][1000 genomes]
rs6822830	0.83[AMR][1000 genomes]
rs6831225	0.83[AMR][1000 genomes]
rs9761048	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv967774	chr4:100025816-100033849	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1840229	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
2	chr4:100020600-100034800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:100020800-100032800	Weak transcription	Fetal Intestine Small	intestine
4	chr4:100020800-100038600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:100021000-100032200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:100021000-100041200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:100025800-100038400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links