Variant report

Variant	rs2239725
Chromosome Location	chr4:3305739-3305740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3297413..3300399-chr4:3305342..3309576,4	MCF-7	breast:
2	chr4:3301249..3303803-chr4:3305446..3308056,2	MCF-7	breast:
3	chr4:3299078..3301560-chr4:3303600..3305932,2	MCF-7	breast:
4	chr4:3294026..3296810-chr4:3301953..3306532,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10155132	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10937924	0.84[EUR][1000 genomes]
rs13104157	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13150241	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2051558	0.90[JPT][hapmap]
rs2071666	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2071671	0.88[CHB][hapmap]
rs2157090	0.84[CHB][hapmap]
rs2236052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2530601	0.84[CHB][hapmap]
rs2748447	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2749778	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2749780	0.84[EUR][1000 genomes]
rs2749781	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2749782	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2749783	1.00[CEU][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2749785	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2798221	0.89[CHB][hapmap]
rs2857982	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3129308	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3129310	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3129314	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3129316	0.88[ASN][1000 genomes]
rs3129327	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap]
rs3129328	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs3129334	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3135145	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3135146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60181496	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs60208975	0.85[EUR][1000 genomes]
rs6446727	0.84[CHB][hapmap]
rs6446731	0.81[CHB][hapmap]
rs6819202	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7435601	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7661630	0.84[CHB][hapmap]
rs881816	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs881817	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs910568	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9996868	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
9	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
10	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
11	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
12	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2239725	DGKQ	cis	parietal	SCAN
rs2239725	RGS12	cis	cerebellum	SCAN
rs2239725	RGS12	cis	brain	BrainEAC

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3294600-3308800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:3296000-3306000	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:3296600-3318600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:3296800-3306800	Weak transcription	Pancreas	Pancrea
5	chr4:3298800-3306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:3299200-3310000	Enhancers	HUVEC	blood vessel
7	chr4:3299600-3306200	Weak transcription	Fetal Intestine Small	intestine
8	chr4:3299600-3306200	Weak transcription	NHLF	lung
9	chr4:3299600-3306600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:3299600-3318600	Weak transcription	Aorta	Aorta
11	chr4:3300600-3306200	Enhancers	Brain Germinal Matrix	brain
12	chr4:3300800-3309000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr4:3301000-3310400	Enhancers	Fetal Muscle Leg	muscle
14	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:3301400-3306200	Weak transcription	Ovary	ovary
16	chr4:3301400-3306400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:3301400-3307000	Weak transcription	Fetal Intestine Large	intestine
18	chr4:3301600-3306400	Weak transcription	Fetal Kidney	kidney
19	chr4:3301600-3312400	Enhancers	Fetal Muscle Trunk	muscle
20	chr4:3301800-3306200	Weak transcription	Adipose Nuclei	Adipose
21	chr4:3301800-3306200	Weak transcription	Right Atrium	heart
22	chr4:3302000-3306000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:3302000-3306200	Weak transcription	Left Ventricle	heart
24	chr4:3302200-3306400	Weak transcription	Psoas Muscle	Psoas
25	chr4:3302400-3306000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:3302400-3306200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:3302400-3306200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:3302600-3306000	Weak transcription	Fetal Lung	lung
29	chr4:3303000-3308000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:3303200-3305800	Enhancers	Primary B cells from peripheral blood	blood
31	chr4:3303200-3306000	Enhancers	Brain Hippocampus Middle	brain
32	chr4:3303200-3306200	Enhancers	Brain Anterior Caudate	brain
33	chr4:3303200-3310800	Enhancers	Fetal Brain Male	brain
34	chr4:3303400-3306600	Weak transcription	Colonic Mucosa	Colon
35	chr4:3303400-3306600	Weak transcription	Right Ventricle	heart
36	chr4:3303600-3310600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr4:3303800-3306800	Weak transcription	Liver	Liver
38	chr4:3304000-3306000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:3304000-3306600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:3304000-3313000	Weak transcription	HepG2	liver
41	chr4:3304200-3308000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr4:3304200-3310600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:3304400-3306200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:3304400-3306200	Weak transcription	NH-A	brain
45	chr4:3304400-3306400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:3304400-3306400	Weak transcription	Osteobl	bone
47	chr4:3304400-3308400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:3304400-3309800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:3304400-3310600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:3304600-3306200	Enhancers	Brain Inferior Temporal Lobe	brain

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