Variant report

Variant	rs2515943
Chromosome Location	chr4:3025015-3025016
allele	A/G
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	CBX3	chr4:3024827-3025158	K562	blood:	n/a	n/a
2	BATF	chr4:3024911-3025139	GM12878	blood:	n/a	chr4:3024990-3025001

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3022979..3027638-chr4:3028157..3033306,5	K562	blood:
2	chr4:3024947..3027361-chr4:3028014..3030506,2	K562	blood:

Variant related genes	Relation type
GRK4	TF binding region
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1018789	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1024323	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs1054090	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs12500735	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12504022	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13120295	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13143902	0.83[ASN][1000 genomes]
rs13146104	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1419044	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1475975	0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs1475976	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1475977	0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs1891710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032463	0.85[CHB][hapmap]
rs2185886	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2256086	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs2342295	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471321	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471325	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs2471326	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471327	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471328	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471336	0.84[TSI][hapmap]
rs2471338	0.84[TSI][hapmap]
rs2471350	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2471351	0.84[TSI][hapmap]
rs2488804	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2488805	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488806	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488809	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs2488815	1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2515932	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2515933	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2960295	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2960308	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3021146	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs6834738	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs729826	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7658707	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7679865	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2515943	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs2515943	GRK4	cis	Artery Tibial	GTEx
rs2515943	ADD1	cis	multi-tissue	Pritchard
rs2515943	GRK4	cis	multi-tissue	Pritchard
rs2515943	GRK4	cis	lung	GTEx
rs2515943	GRK4	cis	Thyroid	GTEx
rs2515943	GRK4	cis	cerebellum	SCAN
rs2515943	NOP14	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2983600-3032000	Weak transcription	Fetal Brain Female	brain
2	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
3	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
4	chr4:3014600-3026200	Weak transcription	Fetal Brain Male	brain
5	chr4:3016200-3033200	Weak transcription	Pancreas	Pancrea
6	chr4:3019200-3039000	Weak transcription	Left Ventricle	heart
7	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
8	chr4:3024600-3025200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
9	chr4:3024600-3025200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:3024600-3025200	ZNF genes & repeats	Brain Angular Gyrus	brain
11	chr4:3024600-3025400	ZNF genes & repeats	HSMMtube	muscle
12	chr4:3024600-3025600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:3024600-3026000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:3024600-3038800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:3024800-3025200	ZNF genes & repeats	Aorta	Aorta
16	chr4:3024800-3025200	ZNF genes & repeats	Fetal Lung	lung
17	chr4:3024800-3025400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:3024800-3029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:3024800-3038800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:3025000-3025200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:3025000-3025200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:3025000-3025400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
23	chr4:3025000-3025600	Strong transcription	Stomach Smooth Muscle	stomach

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