Variant report

Variant	rs2067003
Chromosome Location	chr4:3038639-3038640
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3013109..3014108-chr4:3038245..3039224,2	MCF-7	breast:
2	chr4:2979829..2980854-chr4:3038589..3039659,5	MCF-7	breast:
3	chr4:2949394..2952331-chr4:3037512..3039179,3	MCF-7	breast:
4	chr4:2949602..2950188-chr4:3038243..3039201,2	MCF-7	breast:
5	chr4:3023335..3025840-chr4:3038489..3040216,2	K562	blood:
6	chr4:2934778..2935401-chr4:3038500..3039044,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1263308	0.83[ASN][1000 genomes]
rs1263309	0.85[ASN][1000 genomes]
rs1313766	0.85[ASN][1000 genomes]
rs1313767	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1313769	0.83[ASN][1000 genomes]
rs1313770	0.84[ASN][1000 genomes]
rs1313772	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1313773	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1313774	0.84[ASN][1000 genomes]
rs2471334	0.83[ASN][1000 genomes]
rs2798285	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2798289	0.86[ASN][1000 genomes]
rs2798296	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2857843	0.86[ASN][1000 genomes]
rs2857846	0.86[ASN][1000 genomes]
rs2857847	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2857853	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2857936	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3021126	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3775065	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2067003	GRK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
2	chr4:3019200-3039000	Weak transcription	Left Ventricle	heart
3	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
4	chr4:3024600-3038800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:3024800-3038800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:3025200-3038800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:3025200-3039000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:3025200-3039000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:3025200-3039000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
11	chr4:3025400-3039000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:3025600-3039000	Weak transcription	Fetal Lung	lung
13	chr4:3025600-3042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:3025600-3042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:3029600-3039000	Weak transcription	Brain Anterior Caudate	brain
16	chr4:3032400-3042400	Weak transcription	Fetal Brain Female	brain
17	chr4:3033600-3039000	Weak transcription	Pancreas	Pancrea
18	chr4:3037800-3038800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:3037800-3040000	Enhancers	Fetal Muscle Leg	muscle
20	chr4:3038200-3038800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:3038200-3038800	Flanking Bivalent TSS/Enh	HepG2	liver
22	chr4:3038200-3039000	Weak transcription	HSMMtube	muscle
23	chr4:3038200-3040800	Enhancers	Fetal Muscle Trunk	muscle
24	chr4:3038400-3038800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:3038400-3039000	Enhancers	Duodenum Mucosa	Duodenum
26	chr4:3038400-3040000	Enhancers	Spleen	Spleen
27	chr4:3038400-3040200	Enhancers	Fetal Intestine Small	intestine
28	chr4:3038400-3042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:3038600-3039000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:3038600-3039000	Enhancers	GM12878-XiMat	blood
31	chr4:3038600-3039200	Bivalent Enhancer	K562	blood
32	chr4:3038600-3040200	Enhancers	Colonic Mucosa	Colon
33	chr4:3038600-3040200	Enhancers	Right Ventricle	heart
34	chr4:3038600-3040600	Enhancers	Fetal Heart	heart
35	chr4:3038600-3040600	Enhancers	Gastric	stomach
36	chr4:3038600-3042200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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