Variant report

Variant	rs2602846
Chromosome Location	chr4:100025151-100025152
allele	A/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: 210 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:204)

rs_ID	r²[population]
rs1042364	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1042365	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1126672	0.86[AMR][1000 genomes]
rs1133485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1154400	0.86[AMR][1000 genomes]
rs1154405	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1154406	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1154407	0.82[EUR][1000 genomes]
rs1154410	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1154411	0.85[AFR][1000 genomes]
rs12502237	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12506256	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13102874	0.86[AMR][1000 genomes]
rs13110176	0.86[AMR][1000 genomes]
rs13110764	0.86[AMR][1000 genomes]
rs13112176	0.86[AMR][1000 genomes]
rs13112733	0.86[AMR][1000 genomes]
rs13113166	0.86[AMR][1000 genomes]
rs1311615	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1311616	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1311617	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1311618	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1311619	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1311620	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13127153	0.86[AMR][1000 genomes]
rs13127582	0.86[AMR][1000 genomes]
rs13129488	0.86[AMR][1000 genomes]
rs13132999	0.85[AMR][1000 genomes]
rs13133633	0.86[AMR][1000 genomes]
rs13133647	0.86[AMR][1000 genomes]
rs13138294	0.86[AMR][1000 genomes]
rs13140423	0.86[AMR][1000 genomes]
rs13143133	0.86[AMR][1000 genomes]
rs13146416	0.81[AFR][1000 genomes]
rs1377689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1453872	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1453873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1453874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17217949	0.86[AMR][1000 genomes]
rs17218003	0.86[AMR][1000 genomes]
rs17218073	0.86[AMR][1000 genomes]
rs17218108	0.86[AMR][1000 genomes]
rs17218141	0.86[AMR][1000 genomes]
rs17218162	0.86[AMR][1000 genomes]
rs17218239	0.86[AMR][1000 genomes]
rs17218288	0.86[AMR][1000 genomes]
rs17218560	0.85[AMR][1000 genomes]
rs17218602	0.86[AMR][1000 genomes]
rs17817359	0.86[AMR][1000 genomes]
rs17817868	0.86[AMR][1000 genomes]
rs17817958	0.86[AMR][1000 genomes]
rs1840228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1840229	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1840230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1840231	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1901922	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1984362	0.86[AMR][1000 genomes]
rs1984364	0.86[AMR][1000 genomes]
rs2034696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2213035	0.86[AMR][1000 genomes]
rs2602837	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602840	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2602842	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2602847	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2602851	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602853	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602854	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602855	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2602857	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602858	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2602859	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2602862	0.83[AMR][1000 genomes]
rs2602863	0.80[EUR][1000 genomes]
rs2602865	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2602866	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2602870	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602872	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2602873	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602875	0.83[AMR][1000 genomes]
rs2602876	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2602877	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2602878	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2602881	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602882	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602883	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602888	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2602891	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602893	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602894	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602895	0.86[AMR][1000 genomes]
rs2602896	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602897	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851246	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851247	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851248	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851249	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851252	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851253	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851255	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2851256	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2851257	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2851259	0.83[AMR][1000 genomes]
rs2851260	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2851261	0.88[EUR][1000 genomes]
rs2851263	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2851265	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2851266	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2851267	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2851268	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2851269	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2851272	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2851278	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2851279	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851280	0.84[EUR][1000 genomes]
rs2851281	0.82[EUR][1000 genomes]
rs2851282	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2851283	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2851284	0.84[AMR][1000 genomes]
rs2851286	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28730592	0.81[AFR][1000 genomes]
rs28730595	0.81[AFR][1000 genomes]
rs28730605	0.81[AFR][1000 genomes]
rs28987088	0.86[AMR][1000 genomes]
rs28987097	0.86[AMR][1000 genomes]
rs28987098	0.86[AMR][1000 genomes]
rs28987100	0.86[AMR][1000 genomes]
rs28987101	0.86[AMR][1000 genomes]
rs28987102	0.86[AMR][1000 genomes]
rs29001183	0.86[AMR][1000 genomes]
rs29001194	0.86[AMR][1000 genomes]
rs29001195	0.86[AMR][1000 genomes]
rs29001196	0.82[AMR][1000 genomes]
rs29001199	0.85[AMR][1000 genomes]
rs29001201	0.85[AMR][1000 genomes]
rs29001202	0.86[AMR][1000 genomes]
rs29001203	0.86[AMR][1000 genomes]
rs29001208	0.86[AMR][1000 genomes]
rs29001209	0.86[AMR][1000 genomes]
rs29001211	0.86[AMR][1000 genomes]
rs29001212	0.86[AMR][1000 genomes]
rs29001214	0.86[AMR][1000 genomes]
rs29001215	0.86[AMR][1000 genomes]
rs29001216	0.86[AMR][1000 genomes]
rs29001223	0.86[AMR][1000 genomes]
rs29001224	0.86[AMR][1000 genomes]
rs29001229	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs29001231	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs29001232	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2924580	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2924583	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2924586	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3018046	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3018047	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3018048	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3100629	0.88[AMR][1000 genomes]
rs3100630	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3133152	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3133153	0.82[EUR][1000 genomes]
rs34071486	0.86[AMR][1000 genomes]
rs34360292	0.86[AMR][1000 genomes]
rs34634551	0.86[AMR][1000 genomes]
rs34805407	0.86[AMR][1000 genomes]
rs34876213	0.86[AMR][1000 genomes]
rs34936974	0.86[AMR][1000 genomes]
rs35062722	0.80[AMR][1000 genomes]
rs35073321	0.86[AMR][1000 genomes]
rs35146617	0.82[AMR][1000 genomes]
rs35361391	0.86[AMR][1000 genomes]
rs35491981	0.86[AMR][1000 genomes]
rs35662508	0.86[AMR][1000 genomes]
rs35784540	0.86[AMR][1000 genomes]
rs35797419	0.82[AMR][1000 genomes]
rs35988291	0.86[AMR][1000 genomes]
rs36034266	0.86[AMR][1000 genomes]
rs3919370	0.86[AMR][1000 genomes]
rs4235435	0.83[AMR][1000 genomes]
rs4235436	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4699701	0.81[AFR][1000 genomes]
rs4699712	0.85[AMR][1000 genomes]
rs4699713	0.86[AMR][1000 genomes]
rs4699714	0.86[AMR][1000 genomes]
rs4699716	0.86[AMR][1000 genomes]
rs4699717	0.86[AMR][1000 genomes]
rs4699718	0.86[AMR][1000 genomes]
rs56222233	0.86[AMR][1000 genomes]
rs56272995	0.85[AMR][1000 genomes]
rs56295995	0.85[AMR][1000 genomes]
rs6532779	0.85[EUR][1000 genomes]
rs67311928	0.86[AMR][1000 genomes]
rs6813415	0.86[AMR][1000 genomes]
rs6822830	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6831225	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7434491	0.86[AMR][1000 genomes]
rs7669636	0.86[AMR][1000 genomes]
rs7670060	0.86[AMR][1000 genomes]
rs7670241	0.86[AMR][1000 genomes]
rs7670638	0.86[AMR][1000 genomes]
rs7672728	0.86[AMR][1000 genomes]
rs7683802	0.81[AFR][1000 genomes]
rs7689753	0.86[AMR][1000 genomes]
rs7694646	0.86[AMR][1000 genomes]
rs9761048	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2602846	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:17 , 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	chr4:100021400-100025200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:100022200-100025400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:100023800-100025800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:100024000-100025800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:100024000-100025800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:100024600-100025200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:100024800-100025600	Enhancers	Adipose Nuclei	Adipose
17	chr4:100025000-100025800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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