Variant report

Variant	rs12649553
Chromosome Location	chr4:2911761-2911762
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:2910108-2915436	K562	blood:	n/a	n/a
2	NR2F2	chr4:2911384-2911844	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
2	chr4:2910312..2912100-chr4:2912243..2913801,2	MCF-7	breast:
3	chr4:2910030..2912082-chr4:2925815..2928784,2	MCF-7	breast:
4	chr4:2905184..2907605-chr4:2907928..2912349,4	MCF-7	breast:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000109736	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10026792	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1014947	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1014948	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12623	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263412	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12643323	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12647647	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12647713	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843589	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843603	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17833172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs17833250	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs17833981	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17834203	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877723	1.00[JPT][hapmap]
rs2032470	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2096760	0.82[ASN][1000 genomes]
rs3021131	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35780153	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs55754437	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55927173	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58115360	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59150074	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624833	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6600769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6819310	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6824567	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7436306	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7655104	0.82[AMR][1000 genomes]
rs7678161	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[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	esv1007958	chr4:2904137-2914601	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12649553	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs12649553	GRK4	cis	Thyroid	GTEx
rs12649553	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs12649553	GRK4	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
3	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:2880600-2915000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:2883600-2918600	Strong transcription	Fetal Stomach	stomach
6	chr4:2890400-2918000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:2893000-2919400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:2893200-2914000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:2893200-2918800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr4:2893200-2918800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr4:2893200-2919200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
13	chr4:2893400-2915800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:2893400-2918800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:2893400-2919000	Strong transcription	Fetal Muscle Leg	muscle
16	chr4:2893800-2918600	Strong transcription	Thymus	Thymus
17	chr4:2893800-2919000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr4:2894000-2923000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:2894800-2919800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:2895000-2917800	Strong transcription	Dnd41	blood
21	chr4:2895200-2915000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:2895200-2919000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr4:2895400-2913000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:2895400-2915200	Strong transcription	Placenta	Placenta
25	chr4:2895400-2916200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:2895400-2919000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:2895600-2914000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:2895600-2914200	Strong transcription	GM12878-XiMat	blood
29	chr4:2895600-2915000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:2895600-2918400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:2895600-2919200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:2895600-2919200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:2895800-2919000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:2895800-2919200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:2895800-2919200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:2896400-2911800	Strong transcription	Left Ventricle	heart
37	chr4:2896400-2917000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:2896400-2918000	Strong transcription	HSMMtube	muscle
39	chr4:2896600-2918800	Strong transcription	Adipose Nuclei	Adipose
40	chr4:2896800-2918000	Strong transcription	Spleen	Spleen
41	chr4:2896800-2918800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr4:2897200-2917800	Strong transcription	NHEK	skin
43	chr4:2898600-2917400	Strong transcription	Primary B cells from cord blood	blood
44	chr4:2899800-2918400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:2899800-2919600	Strong transcription	Brain Germinal Matrix	brain
46	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
47	chr4:2903000-2925400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:2903200-2916200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:2903200-2918800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:2903200-2919200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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