Variant report

Variant	rs17833981
Chromosome Location	chr4:2908955-2908956
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:2908950-2909324	K562	blood:	n/a	n/a
2	POLR2A	chr4:2907057-2909711	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
2	chr4:2908128..2910686-chr4:2915793..2918014,2	MCF-7	breast:
3	chr4:2905536..2909706-chr4:2929255..2933631,5	MCF-7	breast:
4	chr4:2756761..2759408-chr4:2907595..2910762,3	MCF-7	breast:
5	chr4:2898305..2901238-chr4:2907549..2909946,2	K562	blood:
6	chr4:2905184..2907605-chr4:2907928..2912349,4	MCF-7	breast:
7	chr4:2747700..2749457-chr4:2908529..2910128,2	MCF-7	breast:
8	chr4:2887075..2889687-chr4:2908396..2910139,2	MCF-7	breast:
9	chr4:2906552..2911481-chr4:2934891..2942965,11	MCF-7	breast:
10	chr4:2907975..2910281-chr4:2941881..2943677,2	MCF-7	breast:

No data

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000249673	Chromatin interaction
ENSG00000109736	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10026792	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs1014947	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1014948	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12623	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263412	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12643323	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12647647	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12647713	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12649553	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557213	0.85[YRI][hapmap]
rs16843589	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843603	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17833172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs17833250	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes]
rs17834203	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877723	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs2032470	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2096760	0.82[ASN][1000 genomes]
rs3021131	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35780153	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.82[ASN][1000 genomes]
rs55754437	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55927173	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58115360	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59150074	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624833	0.83[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs6600769	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6819310	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6824567	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7436306	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7655104	0.82[AMR][1000 genomes]
rs7678161	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.95[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	esv1007958	chr4:2904137-2914601	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs17833981	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs17833981	GRK4	cis	Artery Tibial	GTEx
rs17833981	ADD1	cis	multi-tissue	Pritchard
rs17833981	GRK4	cis	cerebellum	SCAN
rs17833981	TETRAN	cis	multi-tissue	Pritchard
rs17833981	RNF4	cis	cerebellum	SCAN
rs17833981	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs17833981	NOP14	cis	cerebellum	SCAN
rs17833981	CYTL1	cis	parietal	SCAN
rs17833981	LRPAP1	cis	parietal	SCAN
rs17833981	LRPAP1	cis	cerebellum	SCAN
rs17833981	GRK4	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
3	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:2880600-2915000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:2883600-2918600	Strong transcription	Fetal Stomach	stomach
6	chr4:2890400-2918000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:2893000-2919400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:2893200-2914000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:2893200-2918800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr4:2893200-2918800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr4:2893200-2919200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
13	chr4:2893400-2915800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:2893400-2918800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:2893400-2919000	Strong transcription	Fetal Muscle Leg	muscle
16	chr4:2893800-2909200	Strong transcription	Lung	lung
17	chr4:2893800-2918600	Strong transcription	Thymus	Thymus
18	chr4:2893800-2919000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr4:2894000-2923000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:2894800-2919800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:2895000-2917800	Strong transcription	Dnd41	blood
22	chr4:2895200-2915000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:2895200-2919000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:2895400-2913000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:2895400-2915200	Strong transcription	Placenta	Placenta
26	chr4:2895400-2916200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:2895400-2919000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:2895600-2914000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:2895600-2914200	Strong transcription	GM12878-XiMat	blood
30	chr4:2895600-2915000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:2895600-2918400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:2895600-2919200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:2895600-2919200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:2895800-2909000	Strong transcription	Liver	Liver
35	chr4:2895800-2919000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:2895800-2919200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:2895800-2919200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:2896400-2911800	Strong transcription	Left Ventricle	heart
39	chr4:2896400-2917000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:2896400-2918000	Strong transcription	HSMMtube	muscle
41	chr4:2896600-2911400	Strong transcription	Brain Hippocampus Middle	brain
42	chr4:2896600-2918800	Strong transcription	Adipose Nuclei	Adipose
43	chr4:2896800-2911200	Strong transcription	Brain Anterior Caudate	brain
44	chr4:2896800-2918000	Strong transcription	Spleen	Spleen
45	chr4:2896800-2918800	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr4:2897200-2917800	Strong transcription	NHEK	skin
47	chr4:2898600-2917400	Strong transcription	Primary B cells from cord blood	blood
48	chr4:2899800-2918400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:2899800-2919600	Strong transcription	Brain Germinal Matrix	brain
50	chr4:2901200-2910800	Weak transcription	Fetal Heart	heart

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