Variant report

Variant	rs1557213
Chromosome Location	chr4:3038415-3038416
allele	A/G
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	chr4:2949394..2952331-chr4:3037512..3039179,3	MCF-7	breast:
3	chr4:2949602..2950188-chr4:3038243..3039201,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1008210	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1010290	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313768	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1313771	0.91[ASN][1000 genomes]
rs17833981	0.85[YRI][hapmap]
rs17834203	0.85[YRI][hapmap]
rs1801058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071688	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071689	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157097	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187694	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211474	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2471347	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2798286	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2798298	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798304	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857839	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857840	0.99[ASN][1000 genomes]
rs2857841	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857849	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2857852	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6819310	0.85[YRI][hapmap]
rs732859	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]

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
rs1557213	GRK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
2	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
3	chr4:3019200-3039000	Weak transcription	Left Ventricle	heart
4	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
5	chr4:3024600-3038800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:3024800-3038800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:3025200-3038800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:3025200-3039000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:3025200-3039000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:3025200-3039000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
12	chr4:3025400-3039000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:3025600-3039000	Weak transcription	Fetal Lung	lung
14	chr4:3025600-3042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:3025600-3042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:3029600-3039000	Weak transcription	Brain Anterior Caudate	brain
17	chr4:3032400-3042400	Weak transcription	Fetal Brain Female	brain
18	chr4:3033600-3039000	Weak transcription	Pancreas	Pancrea
19	chr4:3033800-3038600	Weak transcription	Gastric	stomach
20	chr4:3035400-3038600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:3037800-3038800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:3037800-3040000	Enhancers	Fetal Muscle Leg	muscle
23	chr4:3038200-3038600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:3038200-3038600	Weak transcription	GM12878-XiMat	blood
25	chr4:3038200-3038800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:3038200-3038800	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr4:3038200-3039000	Weak transcription	HSMMtube	muscle
28	chr4:3038200-3040800	Enhancers	Fetal Muscle Trunk	muscle
29	chr4:3038400-3038800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:3038400-3039000	Enhancers	Duodenum Mucosa	Duodenum
31	chr4:3038400-3040000	Enhancers	Spleen	Spleen
32	chr4:3038400-3040200	Enhancers	Fetal Intestine Small	intestine
33	chr4:3038400-3042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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