Variant report

Variant	rs1801058
Chromosome Location	chr4:3039150-3039151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:3038856..3040749-chr4:3043216..3045055,2	MCF-7	breast:
2	chr4:3013109..3014108-chr4:3038245..3039224,2	MCF-7	breast:
3	chr4:2963384..2966689-chr4:3039150..3042099,3	MCF-7	breast:
4	chr4:3038898..3040591-chr4:3042630..3044225,2	K562	blood:
5	chr4:2979829..2980854-chr4:3038589..3039659,5	MCF-7	breast:
6	chr4:2950371..2951278-chr4:3038861..3039656,2	MCF-7	breast:
7	chr4:2949394..2952331-chr4:3037512..3039179,3	MCF-7	breast:
8	chr4:2980243..2980804-chr4:3039126..3039629,2	MCF-7	breast:
9	chr4:2949602..2950188-chr4:3038243..3039201,2	MCF-7	breast:
10	chr4:3023335..3025840-chr4:3038489..3040216,2	K562	blood:
11	chr4:2962324..2965157-chr4:3038658..3041548,2	K562	blood:
12	chr4:2765604..2766418-chr4:3038748..3039287,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1008210	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1010290	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313768	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1313771	0.91[ASN][1000 genomes]
rs1557213	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071689	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157097	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187694	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211474	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2471347	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2798286	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2798298	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798303	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]
rs2798304	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857839	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857840	0.99[ASN][1000 genomes]
rs2857841	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857849	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2857852	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs732859	0.80[AMR][1000 genomes];0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1801058	ADD1	cis	multi-tissue	Pritchard
rs1801058	GRK4	cis	multi-tissue	Pritchard
rs1801058	GRK4	cis	cerebellum	SCAN
rs1801058	GRK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
2	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
3	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
4	chr4:3025600-3042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:3025600-3042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:3032400-3042400	Weak transcription	Fetal Brain Female	brain
7	chr4:3037800-3040000	Enhancers	Fetal Muscle Leg	muscle
8	chr4:3038200-3040800	Enhancers	Fetal Muscle Trunk	muscle
9	chr4:3038400-3040000	Enhancers	Spleen	Spleen
10	chr4:3038400-3040200	Enhancers	Fetal Intestine Small	intestine
11	chr4:3038400-3042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:3038600-3039200	Bivalent Enhancer	K562	blood
13	chr4:3038600-3040200	Enhancers	Colonic Mucosa	Colon
14	chr4:3038600-3040200	Enhancers	Right Ventricle	heart
15	chr4:3038600-3040600	Enhancers	Fetal Heart	heart
16	chr4:3038600-3040600	Enhancers	Gastric	stomach
17	chr4:3038600-3042200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:3038800-3039200	Enhancers	Primary B cells from peripheral blood	blood
19	chr4:3038800-3039200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr4:3038800-3039200	Enhancers	Adipose Nuclei	Adipose
21	chr4:3038800-3039200	Active TSS	Hela-S3	cervix
22	chr4:3038800-3039200	Flanking Active TSS	HepG2	liver
23	chr4:3038800-3039200	Flanking Active TSS	NHEK	skin
24	chr4:3038800-3039400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr4:3038800-3039400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:3038800-3039400	Enhancers	Brain Cingulate Gyrus	brain
27	chr4:3038800-3039600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:3038800-3039800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:3038800-3039800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr4:3038800-3040000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:3038800-3040000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:3038800-3040200	Enhancers	Liver	Liver
33	chr4:3038800-3040200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr4:3038800-3040200	Enhancers	Placenta	Placenta
35	chr4:3038800-3040600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr4:3038800-3040600	Enhancers	NHDF-Ad	bronchial
37	chr4:3038800-3041000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:3039000-3039200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
39	chr4:3039000-3039200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:3039000-3039200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:3039000-3039200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr4:3039000-3039200	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr4:3039000-3039200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
44	chr4:3039000-3039200	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr4:3039000-3039200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:3039000-3039200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:3039000-3039200	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr4:3039000-3039200	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr4:3039000-3039200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr4:3039000-3039200	Flanking Active TSS	GM12878-XiMat	blood

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