Variant report

Variant	rs2602842
Chromosome Location	chr4:100020476-100020477
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	chr4:100010297..100012013-chr4:100018638..100021523,2	K562	blood:
2	chr4:100008526..100011791-chr4:100020409..100023760,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197894	Chromatin interaction
ENSG00000246090	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1133485	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1154405	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1154406	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1154410	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12506256	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1311615	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311616	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311617	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311618	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311619	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1377689	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1453873	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1453874	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1840228	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1840230	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1840231	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2034696	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602845	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602846	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602847	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602855	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602858	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602859	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602865	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2602866	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2602870	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2602872	0.83[AMR][1000 genomes]
rs2602873	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2602876	0.86[AMR][1000 genomes]
rs2602877	0.86[AMR][1000 genomes]
rs2602878	0.86[AMR][1000 genomes]
rs2602882	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2602883	0.81[AFR][1000 genomes]
rs2602891	0.81[AMR][1000 genomes]
rs2851252	0.83[AMR][1000 genomes]
rs2851253	0.81[AMR][1000 genomes]
rs2851255	0.81[AMR][1000 genomes]
rs2851256	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2851257	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2851260	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2851263	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2851265	0.87[AMR][1000 genomes]
rs2851266	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2851267	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2851268	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2851269	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2851272	0.81[EUR][1000 genomes]
rs2851277	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2851278	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2851282	0.81[AMR][1000 genomes]
rs2851283	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2851286	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2924580	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3018047	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3018048	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4235436	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6822830	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6831225	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9761048	0.87[AMR][1000 genomes];0.84[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	esv1849572	chr4:100007243-100024396	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2602842	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:13 , 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	chr4:100011800-100020600	Weak transcription	Fetal Intestine Small	intestine
4	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
5	chr4:100014000-100022000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:100014400-100021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:100014400-100024000	Weak transcription	HMEC	breast
8	chr4:100020200-100020600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:100020200-100021000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:100020400-100020800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
11	chr4:100020400-100020800	Active TSS	K562	blood
12	chr4:100020400-100021400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:100020400-100024400	Weak transcription	Rectal Mucosa Donor 29	rectum

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