Variant report

Variant	rs17833172
Chromosome Location	chr4:2868514-2868515
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	FOXA2	chr4:2868261-2868557	HepG2	liver:	n/a	n/a
2	CEBPB	chr4:2868271-2868563	HepG2	liver:	n/a	n/a
3	FOXA1	chr4:2868088-2868582	HepG2	liver:	n/a	n/a
4	FOXA1	chr4:2868082-2868677	HepG2	liver:	n/a	n/a
5	FOXA1	chr4:2868153-2868623	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2867681..2870567-chr4:2936383..2939288,2	MCF-7	breast:
2	chr4:2866369..2868735-chr4:2871007..2873229,2	MCF-7	breast:
3	chr4:2865723..2868590-chr4:2936082..2937695,2	MCF-7	breast:
4	chr4:2866956..2870306-chr4:2932983..2937533,4	K562	blood:

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

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10026792	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1014947	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1034400	1.00[CHB][hapmap]
rs12623	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1263412	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12641947	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647713	0.81[AMR][1000 genomes]
rs12649553	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs16843169	1.00[CHB][hapmap]
rs16843481	1.00[CHB][hapmap]
rs16843535	1.00[CHB][hapmap]
rs16843589	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16843596	1.00[CHB][hapmap]
rs16843603	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17833250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17833981	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs17834203	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs1877723	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2032470	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2096760	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs231696	1.00[CHB][hapmap]
rs231706	1.00[CHB][hapmap]
rs2857845	1.00[CHB][hapmap]
rs2858039	1.00[CHB][hapmap]
rs3213502	1.00[CHB][hapmap]
rs35780153	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs41528047	1.00[CHB][hapmap]
rs4690006	1.00[CHB][hapmap]
rs55927173	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58115360	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59150074	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs624833	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6600769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6819310	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824567	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7655104	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678161	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17833172	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs17833172	GRK4	cis	Artery Tibial	GTEx
rs17833172	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs17833172	GRK4	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2857000-2877000	Weak transcription	Dnd41	blood
2	chr4:2857400-2870000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr4:2857400-2877600	Weak transcription	HMEC	breast
4	chr4:2859200-2869400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr4:2860600-2869200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:2860800-2869400	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr4:2860800-2871000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:2861400-2872600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:2862000-2869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:2862000-2869800	Enhancers	Fetal Intestine Small	intestine
11	chr4:2862600-2869800	Enhancers	HepG2	liver
12	chr4:2863000-2869000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:2863000-2869000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:2864000-2869400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:2864200-2869000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:2864600-2868600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:2864600-2869000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:2864600-2869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:2864600-2869200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:2864600-2869200	Enhancers	Brain Hippocampus Middle	brain
21	chr4:2864600-2869400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr4:2864600-2869800	Weak transcription	Thymus	Thymus
23	chr4:2864600-2877400	Weak transcription	NHEK	skin
24	chr4:2864800-2869000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:2864800-2869400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:2864800-2869600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:2864800-2869600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:2864800-2869600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:2864800-2869600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr4:2864800-2869800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:2864800-2869800	Weak transcription	Gastric	stomach
32	chr4:2864800-2873200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:2865000-2868600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:2865000-2868800	Weak transcription	Osteobl	bone
35	chr4:2865000-2869600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:2865400-2868600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:2865400-2868800	Weak transcription	HSMM	muscle
38	chr4:2865400-2868800	Weak transcription	NHDF-Ad	bronchial
39	chr4:2865400-2869000	Weak transcription	HSMMtube	muscle
40	chr4:2865400-2869600	Enhancers	Fetal Lung	lung
41	chr4:2865600-2868800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr4:2865600-2869200	Enhancers	Colon Smooth Muscle	Colon
43	chr4:2865600-2870200	Weak transcription	Placenta	Placenta
44	chr4:2865600-2871200	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:2865600-2871400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:2865800-2869000	Enhancers	Primary B cells from peripheral blood	blood
47	chr4:2866000-2869800	Enhancers	Adipose Nuclei	Adipose
48	chr4:2866200-2869200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr4:2866200-2869200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr4:2866200-2869400	Enhancers	HUES6 Cell Line	embryonic stem cell

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