Variant report

Variant	rs2488809
Chromosome Location	chr4:2948456-2948457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2948442..2950639-chr4:2963524..2965983,2	MCF-7	breast:
2	chr4:2948388..2950164-chr4:2962609..2964597,2	MCF-7	breast:
3	chr4:2945633..2949809-chr4:2953795..2956379,3	K562	blood:

Variant related genes	Relation type
ENSG00000087269	Chromatin interaction
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1018789	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1024323	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1054090	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1063745	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502773	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13120295	0.82[ASN][1000 genomes]
rs1419044	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1475975	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475976	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475977	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891710	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap]
rs1967959	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2022485	0.81[CEU][hapmap]
rs2032463	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2185886	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2256086	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2342295	0.88[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs2471322	0.82[TSI][hapmap]
rs2471327	0.88[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs2471350	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2488806	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2488815	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2515932	0.81[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2515933	0.84[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2515943	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs2515960	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515961	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960295	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2960296	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2960308	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3021145	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021147	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35897740	0.93[ASN][1000 genomes]
rs57191180	0.92[AMR][1000 genomes];0.97[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2488809	RNF4	cis	cerebellum	SCAN
rs2488809	GRK4	cis	cerebellum	SCAN
rs2488809	GRK4	cis	Adipose Subcutaneous	GTEx
rs2488809	ADD1	cis	multi-tissue	Pritchard
rs2488809	GRK4	cis	lung	GTEx
rs2488809	NOP14	cis	cerebellum	SCAN
rs2488809	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs2488809	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs2488809	GRK4	cis	Whole Blood	GTEx
rs2488809	GRK4	cis	multi-tissue	Pritchard
rs2488809	LOC93622	cis	cerebellum	SCAN
rs2488809	GRK4	cis	Artery Tibial	GTEx
rs2488809	GRK4	cis	Thyroid	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	chr4:2938600-2949600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:2938600-2960400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:2938600-2960400	Strong transcription	Brain Cingulate Gyrus	brain
9	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
11	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:2938800-2955600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:2938800-2956800	Strong transcription	Fetal Intestine Large	intestine
14	chr4:2938800-2959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
17	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:2939000-2956800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr4:2939000-2956800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:2939000-2957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:2939000-2958400	Strong transcription	Brain Substantia Nigra	brain
22	chr4:2939000-2960200	Strong transcription	Lung	lung
23	chr4:2939000-2961600	Strong transcription	Fetal Stomach	stomach
24	chr4:2939200-2953800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:2939200-2956200	Strong transcription	Left Ventricle	heart
26	chr4:2939200-2959200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:2939200-2959600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:2939200-2960000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr4:2939200-2960600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:2939200-2961000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr4:2939200-2963200	Weak transcription	Fetal Heart	heart
32	chr4:2939400-2952600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:2939400-2956800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:2939400-2957200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:2939400-2959000	Strong transcription	Ovary	ovary
36	chr4:2939400-2959400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:2939400-2959600	Strong transcription	Adipose Nuclei	Adipose
38	chr4:2939400-2959600	Strong transcription	HUVEC	blood vessel
39	chr4:2939400-2959800	Strong transcription	Fetal Muscle Leg	muscle
40	chr4:2939400-2960000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:2939400-2960400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr4:2939400-2960400	Strong transcription	NHLF	lung
43	chr4:2939400-2960600	Strong transcription	Brain Hippocampus Middle	brain
44	chr4:2939400-2962200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:2939600-2954000	Strong transcription	Pancreas	Pancrea
46	chr4:2939600-2956400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:2939600-2956600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:2939600-2956600	Strong transcription	K562	blood
49	chr4:2939600-2957200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr4:2939600-2957400	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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