Variant report

Variant	rs28721411
Chromosome Location	chr5:16876517-16876518
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16876341..16879051-chr5:16898950..16901260,2	MCF-7	breast:
2	chr5:16875713..16877407-chr5:16911491..16914086,2	MCF-7	breast:
3	chr5:16870568..16873401-chr5:16875593..16878423,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10078199	1.00[AMR][1000 genomes]
rs13362250	1.00[AMR][1000 genomes]
rs28480411	1.00[AMR][1000 genomes]
rs28684838	1.00[AMR][1000 genomes]
rs28697266	1.00[AMR][1000 genomes]
rs73755161	1.00[AMR][1000 genomes]
rs73755170	1.00[AMR][1000 genomes]
rs73755174	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1026773	chr5:16846836-16877367	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1034844	chr5:16854341-16903100	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16865200-16884600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:16865600-16878400	Weak transcription	Fetal Brain Male	brain
3	chr5:16867400-16880600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:16867600-16877400	Weak transcription	Gastric	stomach
5	chr5:16867600-16880800	Weak transcription	Fetal Kidney	kidney
6	chr5:16867600-16883600	Weak transcription	Colonic Mucosa	Colon
7	chr5:16867600-16885800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:16867600-16889000	Weak transcription	Spleen	Spleen
9	chr5:16867800-16878000	Weak transcription	Stomach Mucosa	stomach
10	chr5:16868800-16876600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:16870400-16876800	Weak transcription	Placenta	Placenta
12	chr5:16870600-16879400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:16871200-16886000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:16872200-16877600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:16872400-16877000	Weak transcription	Ovary	ovary
16	chr5:16872400-16877200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:16872400-16877400	Weak transcription	HMEC	breast
18	chr5:16872400-16878400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:16872400-16878800	Weak transcription	Small Intestine	intestine
20	chr5:16872400-16880400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:16872600-16877200	Weak transcription	NHLF	lung
22	chr5:16872600-16877400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:16872600-16877400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:16872800-16877000	Weak transcription	NHDF-Ad	bronchial
25	chr5:16873000-16877800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:16873200-16877800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:16873400-16876600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
28	chr5:16873400-16877400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:16873400-16877800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:16873600-16877800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:16873600-16886000	Weak transcription	Left Ventricle	heart
32	chr5:16874000-16877000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:16874000-16877200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:16874000-16877200	Strong transcription	Fetal Intestine Large	intestine
35	chr5:16874000-16878200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:16874000-16879200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:16874000-16880400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:16874000-16881000	Weak transcription	Liver	Liver
39	chr5:16874000-16881600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:16874000-16894600	Weak transcription	Esophagus	oesophagus
41	chr5:16874200-16880800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:16874200-16883600	Weak transcription	Lung	lung
43	chr5:16874400-16876600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:16874400-16877400	Strong transcription	HUVEC	blood vessel
45	chr5:16874400-16885400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:16874600-16877200	Strong transcription	A549	lung
47	chr5:16874800-16876800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:16874800-16877600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:16874800-16877800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr5:16874800-16880800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links