Variant report

Variant	rs73813209
Chromosome Location	chr5:179753375-179753376
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179753120-179753728	U87	brain:	n/a	n/a
2	POLR2A	chr5:179753251-179753712	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:179753126-179753727	U87	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179740156..179743106-chr5:179752395..179754766,3	MCF-7	breast:
2	chr5:179753055..179755453-chr5:179756186..179759141,2	K562	blood:
3	chr5:179746563..179748878-chr5:179752652..179755339,2	MCF-7	breast:
4	chr5:179752563..179754088-chr5:179754350..179755919,2	K562	blood:

No data

Variant related genes	Relation type
GFPT2	TF binding region
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs58553716	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58646811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59738929	1.00[AMR][1000 genomes]
rs6601115	1.00[AMR][1000 genomes]
rs6884111	1.00[AMR][1000 genomes]
rs73811444	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73811445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73811446	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73811447	1.00[AMR][1000 genomes]
rs73811448	1.00[AMR][1000 genomes]
rs73813208	1.00[AMR][1000 genomes]
rs73813213	1.00[AMR][1000 genomes]
rs73813215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73813217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7735436	1.00[AMR][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	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
4	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
5	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
6	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
7	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
8	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
9	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
11	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
2	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:179727600-179757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
9	chr5:179731600-179755600	Weak transcription	Fetal Brain Female	brain
10	chr5:179738000-179758000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:179738200-179755600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:179739600-179761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:179740400-179757400	Weak transcription	NHLF	lung
14	chr5:179740600-179757600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr5:179741200-179754000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:179741600-179756000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:179741600-179757600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:179741600-179762600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:179741800-179758200	Weak transcription	Fetal Intestine Small	intestine
20	chr5:179742000-179757400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:179742600-179757800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:179743200-179761000	Weak transcription	Right Ventricle	heart
23	chr5:179743400-179754200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:179743400-179758200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:179743800-179756400	Weak transcription	Colonic Mucosa	Colon
26	chr5:179743800-179757400	Weak transcription	Fetal Lung	lung
27	chr5:179744000-179766600	Weak transcription	Gastric	stomach
28	chr5:179746000-179760800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:179746000-179761400	Weak transcription	Right Atrium	heart
30	chr5:179749200-179757400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:179750200-179756600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:179750200-179757400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:179751200-179754200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:179751200-179754200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:179751400-179754400	Weak transcription	Ovary	ovary
36	chr5:179751400-179755000	Weak transcription	Placenta	Placenta
37	chr5:179751600-179755000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:179751600-179755400	Weak transcription	Hela-S3	cervix
39	chr5:179751600-179756200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:179751800-179754400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:179751800-179755600	Weak transcription	Adipose Nuclei	Adipose
42	chr5:179751800-179757400	Weak transcription	HSMMtube	muscle
43	chr5:179752000-179755600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:179752000-179756000	Strong transcription	Osteobl	bone
45	chr5:179752200-179753600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:179752200-179754200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:179752200-179755200	Weak transcription	Brain Anterior Caudate	brain
48	chr5:179752200-179756200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:179752200-179756400	Strong transcription	NH-A	brain
50	chr5:179752200-179759000	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links