Variant report

Variant	rs59028042
Chromosome Location	chr5:179727681-179727682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179720624..179723530-chr5:179725711..179728473,2	K562	blood:
2	chr5:179724952..179726491-chr5:179726777..179728319,2	MCF-7	breast:
3	chr5:179727104..179728705-chr5:179740247..179742971,2	MCF-7	breast:
4	chr5:179716629..179721643-chr5:179722540..179727897,10	K562	blood:

Variant related genes	Relation type
ENSG00000248367	Chromatin interaction
ENSG00000050748	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13161805	1.00[AMR][1000 genomes]
rs1559116	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17080153	0.80[AMR][1000 genomes]
rs35625998	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35690024	1.00[AMR][1000 genomes]
rs35808074	0.83[AMR][1000 genomes]
rs35809530	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3805704	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59666856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61225768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6869542	0.80[AMR][1000 genomes]
rs6872534	0.80[AMR][1000 genomes]
rs73349647	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7702792	0.80[AMR][1000 genomes]
rs7715132	1.00[AMR][1000 genomes]
rs7735336	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
8	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv10787	chr5:179717724-179732388	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179727800	Weak transcription	Aorta	Aorta
2	chr5:179720600-179727800	Weak transcription	Lung	lung
3	chr5:179720600-179728200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr5:179720600-179729600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:179720600-179730400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:179720600-179731400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:179720600-179739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:179720600-179742800	Weak transcription	Right Ventricle	heart
9	chr5:179720600-179743200	Weak transcription	Fetal Lung	lung
10	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
11	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:179720800-179727800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:179720800-179728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:179720800-179730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:179720800-179743600	Weak transcription	Right Atrium	heart
16	chr5:179720800-179747000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:179721000-179727800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:179721000-179727800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:179721000-179728000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:179721000-179728000	Weak transcription	Brain Anterior Caudate	brain
21	chr5:179721000-179728000	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:179721000-179729400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:179721000-179730200	Weak transcription	Brain Angular Gyrus	brain
24	chr5:179721000-179730400	Weak transcription	Adipose Nuclei	Adipose
25	chr5:179721000-179733600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:179721000-179740800	Weak transcription	Esophagus	oesophagus
27	chr5:179721000-179741000	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:179721000-179741200	Weak transcription	Fetal Brain Male	brain
29	chr5:179721000-179743000	Weak transcription	Spleen	Spleen
30	chr5:179721200-179731400	Weak transcription	A549	lung
31	chr5:179721800-179740800	Weak transcription	Gastric	stomach
32	chr5:179722600-179728000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:179723200-179740800	Weak transcription	Pancreas	Pancrea
34	chr5:179723400-179727800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:179723400-179728000	Weak transcription	Fetal Muscle Leg	muscle
36	chr5:179723400-179728200	Weak transcription	Colonic Mucosa	Colon
37	chr5:179723400-179730400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:179723400-179731200	Weak transcription	Brain Germinal Matrix	brain
39	chr5:179723400-179740600	Weak transcription	Fetal Intestine Small	intestine
40	chr5:179723600-179729400	Weak transcription	HSMMtube	muscle
41	chr5:179725200-179740800	Weak transcription	Hela-S3	cervix
42	chr5:179726400-179727800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:179726800-179734800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:179726800-179735000	Strong transcription	Osteobl	bone
45	chr5:179726800-179750600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:179727000-179728800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:179727000-179729000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr5:179727000-179735000	Strong transcription	Fetal Stomach	stomach
49	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:179727200-179728400	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links