Variant report

Variant	rs2071688
Chromosome Location	chr4:3039470-3039471
allele	A/G
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	chr4:2979829..2980854-chr4:3038589..3039659,5	MCF-7	breast:
5	chr4:2950371..2951278-chr4:3038861..3039656,2	MCF-7	breast:
6	chr4:2980243..2980804-chr4:3039126..3039629,2	MCF-7	breast:
7	chr4:3023335..3025840-chr4:3038489..3040216,2	K562	blood:
8	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: 1 )

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

rs_ID	r²[population]
rs1008210	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1010290	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313768	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1313771	0.91[ASN][1000 genomes]
rs1557213	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801058	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071689	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157097	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187694	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187695	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211474	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2471347	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2798286	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2798298	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798303	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798304	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857839	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857840	0.99[ASN][1000 genomes]
rs2857841	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857849	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2857852	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs732859	0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2071688	GRK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 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	chr4:3038600-3040200	Enhancers	Colonic Mucosa	Colon
13	chr4:3038600-3040200	Enhancers	Right Ventricle	heart
14	chr4:3038600-3040600	Enhancers	Fetal Heart	heart
15	chr4:3038600-3040600	Enhancers	Gastric	stomach
16	chr4:3038600-3042200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:3038800-3039600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:3038800-3039800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr4:3038800-3039800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr4:3038800-3040000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:3038800-3040000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:3038800-3040200	Enhancers	Liver	Liver
23	chr4:3038800-3040200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr4:3038800-3040200	Enhancers	Placenta	Placenta
25	chr4:3038800-3040600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr4:3038800-3040600	Enhancers	NHDF-Ad	bronchial
27	chr4:3038800-3041000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:3039000-3039600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr4:3039000-3039600	Active TSS	Rectal Smooth Muscle	rectum
30	chr4:3039000-3039800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:3039000-3039800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:3039000-3039800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:3039000-3039800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:3039000-3039800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:3039000-3039800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr4:3039000-3039800	Active TSS	Brain Substantia Nigra	brain
37	chr4:3039000-3040000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:3039000-3040000	Enhancers	Fetal Thymus	thymus
39	chr4:3039000-3040000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr4:3039000-3040200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr4:3039000-3040200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr4:3039000-3040200	Enhancers	Stomach Mucosa	stomach
43	chr4:3039000-3040400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr4:3039000-3040400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:3039000-3040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:3039000-3040600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:3039000-3040600	Enhancers	Esophagus	oesophagus
48	chr4:3039000-3040600	Enhancers	Left Ventricle	heart
49	chr4:3039000-3040600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr4:3039000-3040600	Enhancers	HSMMtube	muscle

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