Variant report

Variant	rs58115360
Chromosome Location	chr4:2865107-2865108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2859689..2861245-chr4:2862909..2865394,2	MCF-7	breast:
2	chr4:2864305..2866761-chr4:2868243..2869773,2	K562	blood:

Variant related genes	Relation type
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10026792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014948	0.81[AMR][1000 genomes]
rs12623	0.83[ASN][1000 genomes]
rs1263412	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12641947	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12643323	0.81[AMR][1000 genomes]
rs12647647	0.81[AMR][1000 genomes]
rs12647713	0.82[AMR][1000 genomes]
rs12649553	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs16843589	0.83[ASN][1000 genomes]
rs17833172	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17833250	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17833981	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17834203	0.82[AMR][1000 genomes]
rs1877723	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2032470	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2096760	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35780153	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55927173	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59150074	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624833	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6600769	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819310	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6824567	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7655104	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7678161	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs58115360	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs58115360	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs58115360	GRK4	cis	Artery Tibial	GTEx
rs58115360	GRK4	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2852000-2865800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:2857000-2877000	Weak transcription	Dnd41	blood
3	chr4:2857200-2867600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr4:2857400-2870000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr4:2857400-2877600	Weak transcription	HMEC	breast
6	chr4:2857600-2867400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:2858400-2867200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr4:2858800-2865200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr4:2859000-2865200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr4:2859000-2865200	Enhancers	Fetal Muscle Leg	muscle
11	chr4:2859200-2869400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:2859400-2865400	Enhancers	HSMMtube	muscle
13	chr4:2859400-2865800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:2859400-2867200	Enhancers	Small Intestine	intestine
15	chr4:2859600-2865600	Enhancers	Adipose Nuclei	Adipose
16	chr4:2859600-2866000	Enhancers	Duodenum Mucosa	Duodenum
17	chr4:2859800-2865400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:2859800-2865600	Enhancers	Fetal Heart	heart
19	chr4:2859800-2866600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr4:2860000-2867400	Enhancers	Stomach Mucosa	stomach
21	chr4:2860600-2867200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr4:2860600-2869200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:2860800-2865200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr4:2860800-2869400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr4:2860800-2871000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:2861000-2866600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr4:2861200-2865400	Enhancers	HSMM	muscle
28	chr4:2861400-2865200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr4:2861400-2867200	Enhancers	Ovary	ovary
30	chr4:2861400-2872600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:2861600-2865400	Enhancers	NHLF	lung
32	chr4:2861800-2865400	Enhancers	Brain Cingulate Gyrus	brain
33	chr4:2861800-2865400	Enhancers	Fetal Intestine Large	intestine
34	chr4:2861800-2865600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:2862000-2869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:2862000-2869800	Enhancers	Fetal Intestine Small	intestine
37	chr4:2862400-2865400	Enhancers	NH-A	brain
38	chr4:2862400-2867200	Enhancers	Primary B cells from cord blood	blood
39	chr4:2862600-2865600	Enhancers	Placenta	Placenta
40	chr4:2862600-2869800	Enhancers	HepG2	liver
41	chr4:2862800-2865400	Enhancers	Aorta	Aorta
42	chr4:2862800-2865400	Weak transcription	Fetal Brain Female	brain
43	chr4:2862800-2866200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:2862800-2866200	Weak transcription	Fetal Brain Male	brain
45	chr4:2862800-2866600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:2863000-2866800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr4:2863000-2869000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:2863000-2869000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:2863200-2865800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:2863400-2865800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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