Variant report

Variant	rs2515960
Chromosome Location	chr4:2951804-2951805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2950061..2952154-chr4:2953214..2955899,2	K562	blood:
2	chr4:2949394..2952331-chr4:3037512..3039179,3	MCF-7	breast:
3	chr4:2950471..2953919-chr4:2954876..2958140,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1018789	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1024323	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1054090	1.00[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1063745	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502773	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13120295	0.82[ASN][1000 genomes]
rs1419044	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1475975	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475976	0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475977	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891710	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap]
rs1967959	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032463	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2185886	0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2256086	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2342295	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs2471322	0.82[TSI][hapmap]
rs2471327	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs2471350	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2488806	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2488809	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488815	0.92[CHB][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs2515932	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2515933	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2515943	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs2515961	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960295	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2960296	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2960308	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs3021145	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021147	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35897740	0.93[ASN][1000 genomes]
rs57191180	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2515960	GRK4	cis	lung	GTEx
rs2515960	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs2515960	NOP14	cis	cerebellum	SCAN
rs2515960	RNF4	cis	cerebellum	SCAN
rs2515960	GRK4	cis	Thyroid	GTEx
rs2515960	GRK4	cis	Artery Tibial	GTEx
rs2515960	GRK4	cis	cerebellum	SCAN
rs2515960	GRK4	cis	Adipose Subcutaneous	GTEx
rs2515960	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs2515960	GRK4	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2938000-2960400	Weak transcription	Right Atrium	heart
2	chr4:2938200-2962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:2938400-2957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:2938400-2959600	Strong transcription	Brain Anterior Caudate	brain
5	chr4:2938400-2962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:2938600-2960400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:2938600-2960400	Strong transcription	Brain Cingulate Gyrus	brain
8	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
10	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:2938800-2955600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:2938800-2956800	Strong transcription	Fetal Intestine Large	intestine
13	chr4:2938800-2959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:2939000-2956800	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr4:2939000-2956800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:2939000-2957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:2939000-2958400	Strong transcription	Brain Substantia Nigra	brain
21	chr4:2939000-2960200	Strong transcription	Lung	lung
22	chr4:2939000-2961600	Strong transcription	Fetal Stomach	stomach
23	chr4:2939200-2953800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:2939200-2956200	Strong transcription	Left Ventricle	heart
25	chr4:2939200-2959200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:2939200-2959600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:2939200-2960000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr4:2939200-2960600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:2939200-2961000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr4:2939200-2963200	Weak transcription	Fetal Heart	heart
31	chr4:2939400-2952600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:2939400-2956800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:2939400-2957200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:2939400-2959000	Strong transcription	Ovary	ovary
35	chr4:2939400-2959400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:2939400-2959600	Strong transcription	Adipose Nuclei	Adipose
37	chr4:2939400-2959600	Strong transcription	HUVEC	blood vessel
38	chr4:2939400-2959800	Strong transcription	Fetal Muscle Leg	muscle
39	chr4:2939400-2960000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:2939400-2960400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr4:2939400-2960400	Strong transcription	NHLF	lung
42	chr4:2939400-2960600	Strong transcription	Brain Hippocampus Middle	brain
43	chr4:2939400-2962200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:2939600-2954000	Strong transcription	Pancreas	Pancrea
45	chr4:2939600-2956400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:2939600-2956600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:2939600-2956600	Strong transcription	K562	blood
48	chr4:2939600-2957200	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr4:2939600-2957400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:2939600-2957800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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