Variant report

Variant	rs3129314
Chromosome Location	chr4:3293039-3293040
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:3292969-3293111	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:3292258-3296142	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:3292471..3295854-chr4:3462941..3467927,8	MCF-7	breast:
2	chr4:3292102..3294475-chr4:3451973..3453863,2	MCF-7	breast:
3	chr4:3284056..3285844-chr4:3292232..3294141,2	MCF-7	breast:
4	chr4:3233193..3236137-chr4:3292325..3293850,2	MCF-7	breast:
5	chr4:3292635..3294292-chr4:3500969..3502505,2	MCF-7	breast:
6	chr4:3283519..3286259-chr4:3292639..3294370,2	K562	blood:
7	chr4:3292637..3295776-chr4:3483843..3488274,4	MCF-7	breast:
8	chr4:3074885..3077461-chr4:3292207..3294882,2	MCF-7	breast:
9	chr4:3269278..3270856-chr4:3292386..3294072,2	MCF-7	breast:
10	chr4:3292758..3295748-chr4:3341243..3344299,3	MCF-7	breast:

No data

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000159788	Chromatin interaction
ENSG00000175920	Chromatin interaction
ENSG00000251075	Chromatin interaction
ENSG00000197386	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2051558	0.88[EUR][1000 genomes]
rs2071666	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239725	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2749780	0.80[ASN][1000 genomes]
rs2749783	0.85[ASN][1000 genomes]
rs2857861	0.88[EUR][1000 genomes]
rs3129308	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3129310	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3129316	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3135064	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3135145	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3135146	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs910568	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv878460	chr4:3260154-3303976	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr4:3288000-3293200	Weak transcription	Brain Substantia Nigra	brain
2	chr4:3288200-3293200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:3288600-3293200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:3288600-3293200	Weak transcription	Brain Anterior Caudate	brain
5	chr4:3289600-3293200	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:3289600-3293200	Weak transcription	Fetal Lung	lung
7	chr4:3290400-3293200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:3290800-3293200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:3291000-3293200	Weak transcription	Adipose Nuclei	Adipose
10	chr4:3291800-3293400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr4:3292000-3293200	Weak transcription	HUVEC	blood vessel
12	chr4:3292200-3293200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:3292200-3293200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:3292200-3293200	Enhancers	Brain Germinal Matrix	brain
15	chr4:3292200-3293200	Enhancers	Fetal Brain Female	brain
16	chr4:3292200-3293200	Enhancers	Fetal Intestine Large	intestine
17	chr4:3292200-3293200	Enhancers	Left Ventricle	heart
18	chr4:3292200-3293400	Enhancers	Lung	lung
19	chr4:3292200-3293400	Enhancers	Psoas Muscle	Psoas
20	chr4:3292400-3293200	Enhancers	Colonic Mucosa	Colon
21	chr4:3292400-3293200	Enhancers	Pancreas	Pancrea
22	chr4:3292400-3293200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr4:3292400-3293400	Enhancers	Esophagus	oesophagus
24	chr4:3292400-3293400	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr4:3292400-3293400	Enhancers	Right Atrium	heart
26	chr4:3292600-3293200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:3292600-3293200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:3292600-3293200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr4:3292600-3293200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:3292600-3293200	Enhancers	Duodenum Mucosa	Duodenum
31	chr4:3292600-3293200	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr4:3292600-3293200	Enhancers	HMEC	breast
33	chr4:3292600-3293400	Enhancers	Fetal Stomach	stomach
34	chr4:3292600-3293400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr4:3292600-3293400	Enhancers	Spleen	Spleen
36	chr4:3292600-3294000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr4:3292600-3294400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr4:3292600-3295600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:3292800-3293200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
40	chr4:3292800-3293200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:3292800-3293200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:3292800-3293200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:3292800-3293200	Enhancers	Liver	Liver
44	chr4:3292800-3293200	Enhancers	Brain Cingulate Gyrus	brain
45	chr4:3292800-3293200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr4:3292800-3293200	Enhancers	Fetal Intestine Small	intestine
47	chr4:3292800-3293200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr4:3292800-3293400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr4:3292800-3293400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
50	chr4:3292800-3293400	Enhancers	Fetal Heart	heart

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