Variant report

Variant	rs58949283
Chromosome Location	chr4:3370366-3370367
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:3370032-3370520	HepG2	liver:	n/a	n/a
2	CTCF	chr4:3370293-3370376	GM19239	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3368401..3370679-chr4:3386543..3390085,3	MCF-7	breast:
2	chr4:3368324..3371112-chr4:3371223..3374209,2	MCF-7	breast:

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12640186	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640526	0.93[ASN][1000 genomes]
rs12640721	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12643903	0.90[ASN][1000 genomes]
rs16844197	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16844201	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073286	0.93[ASN][1000 genomes]
rs2281470	0.90[ASN][1000 genomes]
rs2343799	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2749775	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749776	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749779	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2749786	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2857859	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2857860	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3129329	0.88[ASN][1000 genomes]
rs3129330	0.89[ASN][1000 genomes]
rs3129331	0.89[ASN][1000 genomes]
rs3129332	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129333	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129336	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62274923	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62274924	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73193371	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73193372	0.94[ASN][1000 genomes]
rs881818	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3339213	chr4:3368054-3372352	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
2	chr4:3363600-3371000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:3364800-3370400	Weak transcription	Pancreas	Pancrea
4	chr4:3364800-3370400	Weak transcription	NHLF	lung
5	chr4:3364800-3370600	Weak transcription	Esophagus	oesophagus
6	chr4:3365000-3371000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:3365600-3370400	Weak transcription	Gastric	stomach
8	chr4:3366000-3370400	Weak transcription	Thymus	Thymus
9	chr4:3366000-3370600	Weak transcription	Colonic Mucosa	Colon
10	chr4:3366400-3370400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:3366400-3370600	Weak transcription	Adipose Nuclei	Adipose
12	chr4:3366600-3370600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:3366800-3370600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:3366800-3372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:3367000-3371200	Enhancers	Fetal Brain Male	brain
16	chr4:3367200-3370400	Weak transcription	Brain Anterior Caudate	brain
17	chr4:3367400-3371000	Weak transcription	Fetal Kidney	kidney
18	chr4:3367400-3371400	Enhancers	Fetal Muscle Leg	muscle
19	chr4:3367600-3370600	Enhancers	Fetal Brain Female	brain
20	chr4:3368000-3371400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:3368000-3373800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:3368200-3371200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr4:3368400-3371000	Weak transcription	Ovary	ovary
24	chr4:3368400-3371400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:3368800-3371000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:3368800-3372400	Enhancers	Lung	lung
27	chr4:3368800-3376800	Enhancers	Spleen	Spleen
28	chr4:3369000-3370400	Weak transcription	Placenta	Placenta
29	chr4:3369000-3370600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:3369000-3370800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr4:3369000-3370800	Weak transcription	Fetal Intestine Large	intestine
32	chr4:3369000-3371000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:3369000-3371200	Enhancers	Fetal Heart	heart
34	chr4:3369200-3370600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:3369200-3370600	Weak transcription	Fetal Intestine Small	intestine
36	chr4:3369200-3370800	Enhancers	Brain Hippocampus Middle	brain
37	chr4:3369200-3371000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:3369200-3371000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:3369200-3374800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:3369400-3370600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:3369400-3370600	Weak transcription	Brain Angular Gyrus	brain
42	chr4:3369400-3370600	Enhancers	Brain Germinal Matrix	brain
43	chr4:3369400-3372800	Weak transcription	HepG2	liver
44	chr4:3369400-3373400	Enhancers	Fetal Stomach	stomach
45	chr4:3369400-3373800	Enhancers	Liver	Liver
46	chr4:3369600-3370800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:3369600-3371600	Enhancers	Fetal Thymus	thymus
48	chr4:3369800-3370800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr4:3369800-3371200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr4:3369800-3371200	Enhancers	HUVEC	blood vessel

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