Variant report

Variant	rs1054090
Chromosome Location	chr4:2943361-2943362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2907975..2910281-chr4:2941881..2943677,2	MCF-7	breast:
2	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
3	chr11:62609089..62610637-chr4:2941968..2944079,2	MCF-7	breast:
4	chr4:2798770..2801758-chr4:2941180..2943976,2	K562	blood:
5	chr4:2844829..2846512-chr4:2941018..2943974,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADD1-1	chr4:2942029-2943596	ENSG00000249673
2	lnc-ADD1-1	chr4:2942029-2943778	ENSG00000249673.2

No data

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000087266	Chromatin interaction
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1018789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1024323	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1063745	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12502773	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1419044	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1419046	0.81[TSI][hapmap]
rs1475975	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1475976	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1475977	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1891710	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap]
rs1967959	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2022485	0.81[CEU][hapmap]
rs2032463	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2051555	0.81[TSI][hapmap]
rs2051556	0.81[TSI][hapmap]
rs2185886	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs2256086	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2342295	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs2471322	0.83[TSI][hapmap]
rs2471327	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap]
rs2471337	0.81[TSI][hapmap]
rs2471340	0.81[TSI][hapmap]
rs2471350	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2488806	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2488809	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]
rs2488815	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2515932	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2515933	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2515943	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs2515960	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2515961	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2960295	0.81[EUR][1000 genomes]
rs2960296	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2960306	0.81[TSI][hapmap]
rs2960308	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs3021140	0.81[TSI][hapmap]
rs3021145	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3021147	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35897740	0.87[ASN][1000 genomes]
rs57191180	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	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	esv3375632	chr4:2941604-2944102	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1054090	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs1054090	RNF4	cis	cerebellum	SCAN
rs1054090	LOC93622	cis	cerebellum	SCAN
rs1054090	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs1054090	GRK4	cis	Artery Tibial	GTEx
rs1054090	GRK4	cis	Adipose Subcutaneous	GTEx
rs1054090	GRK4	cis	cerebellum	SCAN
rs1054090	GRK4	cis	Thyroid	GTEx
rs1054090	NOP14	cis	cerebellum	SCAN
rs1054090	GRK4	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2937800-2945800	Weak transcription	Fetal Kidney	kidney
2	chr4:2938000-2945400	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr4:2938000-2960400	Weak transcription	Right Atrium	heart
4	chr4:2938200-2946800	Strong transcription	Thymus	Thymus
5	chr4:2938200-2948400	Strong transcription	Fetal Intestine Small	intestine
6	chr4:2938200-2962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:2938400-2944400	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:2938400-2957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:2938400-2959600	Strong transcription	Brain Anterior Caudate	brain
10	chr4:2938400-2962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:2938600-2943800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr4:2938600-2949600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:2938600-2960400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:2938600-2960400	Strong transcription	Brain Cingulate Gyrus	brain
15	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
17	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:2938800-2944000	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr4:2938800-2955600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:2938800-2956800	Strong transcription	Fetal Intestine Large	intestine
21	chr4:2938800-2959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:2939000-2956800	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr4:2939000-2956800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:2939000-2957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:2939000-2958400	Strong transcription	Brain Substantia Nigra	brain
29	chr4:2939000-2960200	Strong transcription	Lung	lung
30	chr4:2939000-2961600	Strong transcription	Fetal Stomach	stomach
31	chr4:2939200-2953800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:2939200-2956200	Strong transcription	Left Ventricle	heart
33	chr4:2939200-2959200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:2939200-2959600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:2939200-2960000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr4:2939200-2960600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:2939200-2961000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr4:2939200-2963200	Weak transcription	Fetal Heart	heart
39	chr4:2939400-2944200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr4:2939400-2945800	Strong transcription	HSMMtube	muscle
41	chr4:2939400-2948000	Strong transcription	Liver	Liver
42	chr4:2939400-2952600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:2939400-2956800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:2939400-2957200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:2939400-2959000	Strong transcription	Ovary	ovary
46	chr4:2939400-2959400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:2939400-2959600	Strong transcription	Adipose Nuclei	Adipose
48	chr4:2939400-2959600	Strong transcription	HUVEC	blood vessel
49	chr4:2939400-2959800	Strong transcription	Fetal Muscle Leg	muscle
50	chr4:2939400-2960000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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