Variant report

Variant	rs2515963
Chromosome Location	chr4:2960430-2960431
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	WRNIP1	chr4:2960152-2960659	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2948727..2950755-chr4:2959506..2963214,4	K562	blood:
2	chr4:2959980..2962211-chr4:2969909..2971816,3	MCF-7	breast:
3	chr4:2960088..2962960-chr4:3074155..3076323,2	MCF-7	breast:

Variant related genes	Relation type
GRK4	TF binding region
ENSG00000251075	Chromatin interaction
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10021191	0.83[ASN][1000 genomes]
rs10030130	0.83[ASN][1000 genomes]
rs1056094	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12643541	0.83[ASN][1000 genomes]
rs13114014	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419046	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs1475974	0.91[EUR][1000 genomes]
rs16843629	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16843684	0.83[ASN][1000 genomes]
rs2022485	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2040061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2051555	0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs2051556	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs2051557	0.81[ASN][1000 genomes]
rs2153997	0.83[ASN][1000 genomes]
rs2185887	0.83[ASN][1000 genomes]
rs2185888	0.83[ASN][1000 genomes]
rs2251457	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs2471322	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs2471323	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2471324	0.86[CEU][hapmap];0.83[ASN][1000 genomes]
rs2471325	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.80[EUR][1000 genomes]
rs2471335	0.83[ASN][1000 genomes]
rs2471336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2471337	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs2471338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2471339	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2471340	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs2471346	0.83[ASN][1000 genomes]
rs2471349	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2471351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2488813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs2488816	0.83[ASN][1000 genomes]
rs2488817	0.83[ASN][1000 genomes]
rs2488818	0.81[ASN][1000 genomes]
rs2515935	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2515936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2515938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2515939	0.83[ASN][1000 genomes]
rs2515940	0.83[ASN][1000 genomes]
rs2515941	0.83[ASN][1000 genomes]
rs2515942	0.83[ASN][1000 genomes]
rs28414352	0.83[ASN][1000 genomes]
rs28666534	0.83[ASN][1000 genomes]
rs2960298	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2960303	0.81[ASN][1000 genomes]
rs2960306	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs2960307	0.83[ASN][1000 genomes]
rs2960310	0.83[ASN][1000 genomes]
rs2995797	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2995803	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2995804	0.83[ASN][1000 genomes]
rs3021136	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3021138	0.83[ASN][1000 genomes]
rs3021139	0.83[ASN][1000 genomes]
rs3021140	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs3021141	0.83[ASN][1000 genomes]
rs3021142	0.83[ASN][1000 genomes]
rs3021146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56214407	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446720	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7667520	0.83[ASN][1000 genomes]
rs7678019	0.83[ASN][1000 genomes]
rs7690813	0.83[ASN][1000 genomes]
rs7696434	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1008527	chr4:2957814-3019042	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1014013	chr4:2959876-3009507	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv536999	chr4:2959876-3009507	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2515963	GRK4	cis	parietal	SCAN
rs2515963	GRK4	cis	Thyroid	GTEx
rs2515963	GRK4	cis	Artery Aorta	GTEx
rs2515963	NOP14	cis	cerebellum	SCAN
rs2515963	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs2515963	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs2515963	GRK4	cis	Adipose Subcutaneous	GTEx
rs2515963	GRK4	cis	lung	GTEx
rs2515963	GRK4	cis	Artery Tibial	GTEx
rs2515963	GRK4	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2938200-2962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:2938400-2962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
5	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
8	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:2939000-2961600	Strong transcription	Fetal Stomach	stomach
10	chr4:2939200-2960600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:2939200-2961000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:2939200-2963200	Weak transcription	Fetal Heart	heart
13	chr4:2939400-2960600	Strong transcription	Brain Hippocampus Middle	brain
14	chr4:2939400-2962200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:2939600-2960800	Strong transcription	Fetal Brain Female	brain
16	chr4:2939600-2961400	Strong transcription	Dnd41	blood
17	chr4:2939600-2961600	Strong transcription	Fetal Thymus	thymus
18	chr4:2939800-2960600	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr4:2939800-2960600	Strong transcription	HepG2	liver
20	chr4:2940000-2962200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr4:2945200-2960600	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:2945400-2960600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr4:2945400-2961600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:2947200-2960600	Strong transcription	Thymus	Thymus
25	chr4:2948800-2963200	Strong transcription	Fetal Intestine Small	intestine
26	chr4:2949000-2961600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr4:2951800-2960600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:2953600-2963200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:2954400-2962400	Strong transcription	A549	lung
30	chr4:2954800-2960800	Strong transcription	Hela-S3	cervix
31	chr4:2956000-2963200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:2956800-2960800	Strong transcription	Left Ventricle	heart
33	chr4:2957000-2960800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:2957200-2960600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:2957200-2960600	Strong transcription	Fetal Lung	lung
36	chr4:2957600-2960600	Strong transcription	Right Ventricle	heart
37	chr4:2957600-2961600	Strong transcription	Primary B cells from cord blood	blood
38	chr4:2957600-2961800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:2957600-2962200	Strong transcription	Fetal Intestine Large	intestine
40	chr4:2957800-2961600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr4:2958000-2960800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr4:2958200-2961600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:2958200-2962200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:2958200-2963200	Weak transcription	Stomach Mucosa	stomach
45	chr4:2958400-2960600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:2958400-2963000	Strong transcription	K562	blood
47	chr4:2958400-2963200	Weak transcription	Brain Substantia Nigra	brain
48	chr4:2958400-2963200	Weak transcription	Fetal Brain Male	brain
49	chr4:2958400-2963200	Weak transcription	Fetal Kidney	kidney
50	chr4:2958600-2960600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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