Variant report

Variant	rs2798303
Chromosome Location	chr4:3040587-3040588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3038856..3040749-chr4:3043216..3045055,2	MCF-7	breast:
2	chr4:2963384..2966689-chr4:3039150..3042099,3	MCF-7	breast:
3	chr4:3038898..3040591-chr4:3042630..3044225,2	K562	blood:
4	chr4:2962324..2965157-chr4:3038658..3041548,2	K562	blood:

Variant related genes	Relation type
ENSG00000087269	Chromatin interaction
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1008210	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1010290	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1313768	0.91[ASN][1000 genomes]
rs1313771	0.90[ASN][1000 genomes]
rs1557213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1801058	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071688	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071689	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2157097	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2187694	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187695	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2211474	0.90[ASN][1000 genomes]
rs2471347	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2798286	0.92[ASN][1000 genomes]
rs2798298	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798304	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857839	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857840	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857841	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857849	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2857852	0.89[ASN][1000 genomes]
rs732859	0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2798303	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs2798303	GRK4	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
2	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
3	chr4:3025600-3042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:3025600-3042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:3032400-3042400	Weak transcription	Fetal Brain Female	brain
6	chr4:3038200-3040800	Enhancers	Fetal Muscle Trunk	muscle
7	chr4:3038400-3042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:3038600-3040600	Enhancers	Fetal Heart	heart
9	chr4:3038600-3040600	Enhancers	Gastric	stomach
10	chr4:3038600-3042200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:3038800-3040600	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr4:3038800-3040600	Enhancers	NHDF-Ad	bronchial
13	chr4:3038800-3041000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:3039000-3040600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:3039000-3040600	Enhancers	Esophagus	oesophagus
16	chr4:3039000-3040600	Enhancers	Left Ventricle	heart
17	chr4:3039000-3040600	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr4:3039000-3040600	Enhancers	HSMMtube	muscle
19	chr4:3039200-3040600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:3039200-3040600	Enhancers	HSMM	muscle
21	chr4:3039400-3040600	Enhancers	Fetal Lung	lung
22	chr4:3039400-3042800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:3039400-3043000	Weak transcription	Pancreas	Pancrea
24	chr4:3039600-3040600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr4:3039600-3040600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr4:3039600-3040600	Enhancers	Lung	lung
27	chr4:3039600-3040600	Flanking Active TSS	GM12878-XiMat	blood
28	chr4:3039600-3042800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:3039800-3040600	Enhancers	Small Intestine	intestine
30	chr4:3039800-3040600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr4:3039800-3043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:3039800-3043000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:3039800-3043200	Weak transcription	Fetal Kidney	kidney
34	chr4:3040000-3042200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:3040000-3042400	Weak transcription	Spleen	Spleen
36	chr4:3040000-3042600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:3040000-3043000	Weak transcription	Psoas Muscle	Psoas
38	chr4:3040000-3043000	Weak transcription	Right Atrium	heart
39	chr4:3040200-3040600	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:3040200-3040600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr4:3040200-3040600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:3040200-3040600	Enhancers	Duodenum Mucosa	Duodenum
43	chr4:3040200-3040600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr4:3040200-3041400	Enhancers	Fetal Muscle Leg	muscle
45	chr4:3040200-3041600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:3040200-3041800	Enhancers	Primary B cells from peripheral blood	blood
47	chr4:3040200-3042400	Weak transcription	Colonic Mucosa	Colon
48	chr4:3040200-3042400	Weak transcription	Placenta	Placenta
49	chr4:3040200-3042600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:3040200-3042800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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