Variant report

Variant	rs2851281
Chromosome Location	chr4:100020944-100020945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100008642..100013321-chr4:100020625..100023682,5	MCF-7	breast:
2	chr4:99915817..99917521-chr4:100020700..100022232,2	MCF-7	breast:
3	chr4:100010297..100012013-chr4:100018638..100021523,2	K562	blood:
4	chr4:100008526..100011791-chr4:100020409..100023760,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197894	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000246090	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1133485	0.82[EUR][1000 genomes]
rs1377689	0.82[EUR][1000 genomes]
rs1453873	0.81[EUR][1000 genomes]
rs1453874	0.82[EUR][1000 genomes]
rs1840228	0.82[EUR][1000 genomes]
rs1840230	0.82[EUR][1000 genomes]
rs1840231	0.83[EUR][1000 genomes]
rs2034696	0.82[EUR][1000 genomes]
rs2602845	0.82[EUR][1000 genomes]
rs2602846	0.82[EUR][1000 genomes]
rs2602847	0.82[EUR][1000 genomes]
rs2602855	0.82[EUR][1000 genomes]
rs2602858	0.82[EUR][1000 genomes]
rs2602859	0.82[EUR][1000 genomes]
rs2602863	0.81[EUR][1000 genomes]
rs2851261	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2851262	0.80[AMR][1000 genomes]
rs2851263	0.82[EUR][1000 genomes]
rs2851266	0.80[EUR][1000 genomes]
rs2851267	0.81[EUR][1000 genomes]
rs2851268	0.82[EUR][1000 genomes]
rs2851269	0.82[EUR][1000 genomes]
rs2851272	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2851277	0.82[EUR][1000 genomes]
rs2851278	0.82[EUR][1000 genomes]
rs2851280	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2851283	0.81[EUR][1000 genomes]
rs2924580	0.81[EUR][1000 genomes]
rs3133153	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6532779	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6532780	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6532782	0.82[AMR][1000 genomes]
rs6823907	0.89[AMR][1000 genomes]
rs7375598	0.83[AMR][1000 genomes]
rs7375618	0.82[AMR][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
rs2851281	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:19 , 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	chr4:100014000-100022000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:100014400-100021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:100014400-100024000	Weak transcription	HMEC	breast
7	chr4:100020200-100021000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:100020400-100021400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:100020400-100024400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:100020600-100021000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:100020600-100021000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:100020600-100021800	Enhancers	Placenta	Placenta
13	chr4:100020600-100022200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr4:100020600-100034800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:100020800-100021400	Flanking Active TSS	K562	blood
16	chr4:100020800-100022200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:100020800-100022800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr4:100020800-100032800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:100020800-100038600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links