Variant report

Variant	rs4700943
Chromosome Location	chr5:179761248-179761249
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179760391-179762871	U87	brain:	n/a	n/a
2	POLR2A	chr5:179760453-179761682	U87	brain:	n/a	n/a
3	POLR2A	chr5:179760515-179761606	U87	brain:	n/a	n/a
4	GATA3	chr5:179760391-179761291	A549	lung:	n/a	n/a
5	EP300	chr5:179760412-179761284	A549	lung:	n/a	n/a
6	POLR2A	chr5:179760453-179761330	U87	brain:	n/a	n/a
7	POLR2A	chr5:179760970-179761325	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr5:179760446-179761612	A549	lung:	n/a	n/a
9	E2F6	chr5:179760454-179761315	A549	lung:	n/a	n/a
10	MAX	chr5:179760432-179761497	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179760436..179761974-chr5:179802802..179805254,2	MCF-7	breast:
2	chr5:179761022..179762666-chr5:179778358..179780120,2	MCF-7	breast:
3	chr5:179720130..179723028-chr5:179758867..179761631,2	MCF-7	breast:
4	chr5:179758082..179759697-chr5:179760362..179762379,2	MCF-7	breast:
5	chr5:179761126..179762815-chr5:179764028..179766885,2	MCF-7	breast:

No data

Variant related genes	Relation type
GFPT2	TF binding region
ENSG00000248367	Chromatin interaction
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1078646	0.89[ASN][1000 genomes]
rs1559114	0.90[ASN][1000 genomes]
rs17080196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17080199	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235511	0.88[ASN][1000 genomes]
rs4566752	0.90[ASN][1000 genomes]
rs4700736	0.88[ASN][1000 genomes]
rs62404950	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404953	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62404956	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62404958	0.88[ASN][1000 genomes]
rs62404959	0.89[ASN][1000 genomes]
rs62406364	0.83[ASN][1000 genomes]
rs6601110	1.00[ASN][1000 genomes]
rs6859159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864729	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871454	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884276	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6899097	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72811045	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811049	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686940	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
12	nsv883291	chr5:179755559-179818868	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv984575	chr5:179759624-179791220	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
2	chr5:179741600-179762600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:179744000-179766600	Weak transcription	Gastric	stomach
4	chr5:179746000-179761400	Weak transcription	Right Atrium	heart
5	chr5:179756200-179761600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:179757000-179779000	Weak transcription	Esophagus	oesophagus
7	chr5:179757800-179765600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:179758600-179761400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:179759000-179761400	Weak transcription	Fetal Lung	lung
10	chr5:179759000-179762800	Weak transcription	Pancreas	Pancrea
11	chr5:179759000-179764600	Weak transcription	Left Ventricle	heart
12	chr5:179759000-179766600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:179759000-179770200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:179759200-179767800	Weak transcription	Fetal Intestine Small	intestine
15	chr5:179759600-179762800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:179759600-179766600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr5:179759800-179761400	Weak transcription	Placenta	Placenta
18	chr5:179759800-179761800	Enhancers	HSMM	muscle
19	chr5:179759800-179762400	Weak transcription	Fetal Intestine Large	intestine
20	chr5:179759800-179766000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:179759800-179767200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:179760000-179765600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:179760000-179765800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:179760200-179765400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:179760400-179761800	Enhancers	NHDF-Ad	bronchial
26	chr5:179760400-179765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:179760400-179765800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:179760400-179767000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:179760600-179761600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:179760600-179761600	Flanking Active TSS	Hela-S3	cervix
31	chr5:179760600-179764200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:179760600-179764800	Strong transcription	Brain Anterior Caudate	brain
33	chr5:179760600-179765000	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr5:179760600-179765400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:179760600-179765600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr5:179760600-179765800	Strong transcription	Fetal Muscle Leg	muscle
37	chr5:179760600-179766000	Strong transcription	Fetal Stomach	stomach
38	chr5:179760600-179767000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:179760800-179761400	ZNF genes & repeats	Lung	lung
40	chr5:179760800-179761600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:179760800-179761600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:179760800-179761600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:179760800-179761600	Enhancers	HSMMtube	muscle
44	chr5:179760800-179762200	Genic enhancers	Adipose Nuclei	Adipose
45	chr5:179760800-179763000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:179760800-179763200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:179760800-179763600	Strong transcription	Brain Substantia Nigra	brain
48	chr5:179760800-179764000	Strong transcription	Brain Germinal Matrix	brain
49	chr5:179760800-179764800	Strong transcription	Brain Cingulate Gyrus	brain
50	chr5:179760800-179765200	Strong transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links