Variant report

Variant	rs2602862
Chromosome Location	chr4:100033221-100033222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 167 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1042364	0.81[EUR][1000 genomes]
rs1042365	0.81[EUR][1000 genomes]
rs1126672	0.80[EUR][1000 genomes]
rs1133485	0.83[AMR][1000 genomes]
rs1154400	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1154401	0.89[AFR][1000 genomes]
rs1154403	0.82[EUR][1000 genomes]
rs12502237	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13102874	0.80[EUR][1000 genomes]
rs13107558	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13110176	0.80[EUR][1000 genomes]
rs13110764	0.80[EUR][1000 genomes]
rs13112176	0.80[EUR][1000 genomes]
rs13112733	0.80[EUR][1000 genomes]
rs13113166	0.80[EUR][1000 genomes]
rs1311620	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13127153	0.80[EUR][1000 genomes]
rs13127582	0.80[EUR][1000 genomes]
rs13129488	0.80[EUR][1000 genomes]
rs13133647	0.80[EUR][1000 genomes]
rs13138294	0.80[EUR][1000 genomes]
rs13140423	0.80[EUR][1000 genomes]
rs13143133	0.80[EUR][1000 genomes]
rs1377689	0.83[AMR][1000 genomes]
rs1453872	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1453873	0.83[AMR][1000 genomes]
rs1453874	0.83[AMR][1000 genomes]
rs17217949	0.80[EUR][1000 genomes]
rs17218003	0.80[EUR][1000 genomes]
rs17218073	0.80[EUR][1000 genomes]
rs17218108	0.80[EUR][1000 genomes]
rs17218141	0.80[EUR][1000 genomes]
rs17218162	0.80[EUR][1000 genomes]
rs17218239	0.80[EUR][1000 genomes]
rs17218288	0.80[EUR][1000 genomes]
rs17218560	0.80[EUR][1000 genomes]
rs17218602	0.80[EUR][1000 genomes]
rs17817359	0.80[EUR][1000 genomes]
rs17817868	0.80[EUR][1000 genomes]
rs17817958	0.80[EUR][1000 genomes]
rs1840228	0.83[AMR][1000 genomes]
rs1840229	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1840230	0.83[AMR][1000 genomes]
rs1840231	0.86[AMR][1000 genomes]
rs1901922	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2034696	0.83[AMR][1000 genomes]
rs2602840	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2602845	0.83[AMR][1000 genomes]
rs2602846	0.83[AMR][1000 genomes]
rs2602851	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2602853	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2602854	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2602855	0.86[AMR][1000 genomes]
rs2602856	0.97[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2602857	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2602858	0.86[AMR][1000 genomes]
rs2602859	0.86[AMR][1000 genomes]
rs2602860	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2602865	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602866	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602868	0.83[AFR][1000 genomes]
rs2602870	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602872	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602873	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602875	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2602876	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602877	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602878	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602881	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2602882	0.83[AMR][1000 genomes]
rs2602883	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2602888	0.81[AMR][1000 genomes]
rs2602891	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2602893	0.82[EUR][1000 genomes]
rs2602894	0.81[EUR][1000 genomes]
rs2602895	0.80[EUR][1000 genomes]
rs2602896	0.81[EUR][1000 genomes]
rs2602897	0.81[EUR][1000 genomes]
rs2851246	0.81[EUR][1000 genomes]
rs2851247	0.81[EUR][1000 genomes]
rs2851248	0.81[EUR][1000 genomes]
rs2851249	0.81[EUR][1000 genomes]
rs2851252	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2851253	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2851255	0.83[AMR][1000 genomes]
rs2851256	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851257	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851259	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2851260	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2851263	0.86[AMR][1000 genomes]
rs2851265	0.86[AMR][1000 genomes]
rs2851267	0.86[AMR][1000 genomes]
rs2851268	0.86[AMR][1000 genomes]
rs2851269	0.86[AMR][1000 genomes]
rs2851270	0.97[AFR][1000 genomes]
rs2851274	0.97[AFR][1000 genomes]
rs2851277	0.83[AMR][1000 genomes]
rs2851278	0.83[AMR][1000 genomes]
rs2851279	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2851284	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28987088	0.80[EUR][1000 genomes]
rs28987097	0.80[EUR][1000 genomes]
rs28987098	0.80[EUR][1000 genomes]
rs28987100	0.80[EUR][1000 genomes]
rs28987102	0.80[EUR][1000 genomes]
rs29001183	0.80[EUR][1000 genomes]
rs29001194	0.80[EUR][1000 genomes]
rs29001195	0.80[EUR][1000 genomes]
rs29001196	0.80[EUR][1000 genomes]
rs29001199	0.80[EUR][1000 genomes]
rs29001201	0.80[EUR][1000 genomes]
rs29001203	0.80[EUR][1000 genomes]
rs29001208	0.80[EUR][1000 genomes]
rs29001209	0.80[EUR][1000 genomes]
rs29001211	0.80[EUR][1000 genomes]
rs29001212	0.80[EUR][1000 genomes]
rs29001214	0.80[EUR][1000 genomes]
rs29001215	0.80[EUR][1000 genomes]
rs29001216	0.80[EUR][1000 genomes]
rs29001223	0.80[EUR][1000 genomes]
rs29001224	0.80[EUR][1000 genomes]
rs29001229	0.81[EUR][1000 genomes]
rs29001231	0.81[EUR][1000 genomes]
rs29001232	0.81[EUR][1000 genomes]
rs2924580	0.89[AMR][1000 genomes]
rs2924583	0.81[EUR][1000 genomes]
rs2924585	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2924586	0.82[AMR][1000 genomes]
rs3018046	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3100630	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3133152	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34071486	0.80[EUR][1000 genomes]
rs34360292	0.80[EUR][1000 genomes]
rs34805407	0.80[EUR][1000 genomes]
rs34876213	0.80[EUR][1000 genomes]
rs34936974	0.80[EUR][1000 genomes]
rs35073321	0.80[EUR][1000 genomes]
rs35146617	0.81[AMR][1000 genomes]
rs35662508	0.80[EUR][1000 genomes]
rs35784540	0.80[EUR][1000 genomes]
rs35988291	0.80[EUR][1000 genomes]
rs36034266	0.80[EUR][1000 genomes]
rs3919370	0.80[EUR][1000 genomes]
rs4235435	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4235436	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4699713	0.80[EUR][1000 genomes]
rs4699714	0.80[EUR][1000 genomes]
rs56272995	0.80[EUR][1000 genomes]
rs56295995	0.80[EUR][1000 genomes]
rs67311928	0.80[EUR][1000 genomes]
rs6813415	0.80[EUR][1000 genomes]
rs6831257	0.84[AFR][1000 genomes]
rs7669636	0.80[EUR][1000 genomes]
rs7670060	0.80[EUR][1000 genomes]
rs7670638	0.80[EUR][1000 genomes]
rs7672728	0.80[EUR][1000 genomes]
rs7689753	0.80[EUR][1000 genomes]
rs7694646	0.80[EUR][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
rs2602862	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:6 , 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	chr4:100020800-100038600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:100021000-100041200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	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