Variant report

Variant	rs6819310
Chromosome Location	chr4:2869127-2869128
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	ZNF263	chr4:2869083-2870005	HEK293-T-REx	kidney:	n/a	chr4:2869533-2869554 chr4:2869415-2869424
2	POLR2A	chr4:2868831-2869878	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2868702..2870783-chr4:2881589..2883580,3	K562	blood:
2	chr4:2867681..2870567-chr4:2936383..2939288,2	MCF-7	breast:
3	chr4:2866956..2870306-chr4:2932983..2937533,4	K562	blood:

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

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10026792	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1014947	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1014948	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12623	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1263412	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12641947	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12643323	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12647647	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12647713	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12649553	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1557213	0.85[YRI][hapmap]
rs16843589	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16843603	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17833172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17833250	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17833981	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]
rs17834203	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1877723	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2032470	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096760	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3021131	0.82[EUR][1000 genomes]
rs35780153	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55927173	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58115360	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59150074	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624833	0.83[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6600769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6824567	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7436306	0.80[EUR][1000 genomes]
rs7655104	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7678161	0.83[CEU][hapmap];1.00[JPT][hapmap]

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
rs6819310	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs6819310	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs6819310	GRK4	cis	Artery Tibial	GTEx
rs6819310	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	chr4:2864000-2869400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:2864600-2869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:2864600-2869200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:2864600-2869200	Enhancers	Brain Hippocampus Middle	brain
16	chr4:2864600-2869400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr4:2864600-2869800	Weak transcription	Thymus	Thymus
18	chr4:2864600-2877400	Weak transcription	NHEK	skin
19	chr4:2864800-2869400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:2864800-2869600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:2864800-2869600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:2864800-2869600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:2864800-2869600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr4:2864800-2869800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:2864800-2869800	Weak transcription	Gastric	stomach
26	chr4:2864800-2873200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:2865000-2869600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:2865400-2869600	Enhancers	Fetal Lung	lung
29	chr4:2865600-2869200	Enhancers	Colon Smooth Muscle	Colon
30	chr4:2865600-2870200	Weak transcription	Placenta	Placenta
31	chr4:2865600-2871200	Enhancers	Primary hematopoietic stem cells	blood
32	chr4:2865600-2871400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:2866000-2869800	Enhancers	Adipose Nuclei	Adipose
34	chr4:2866200-2869200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr4:2866200-2869200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr4:2866200-2869400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:2866200-2869600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr4:2866200-2869600	Enhancers	Brain Substantia Nigra	brain
39	chr4:2866200-2869800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:2866200-2869800	Enhancers	Liver	Liver
41	chr4:2866200-2869800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr4:2866200-2872400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:2866400-2869400	Enhancers	Stomach Smooth Muscle	stomach
44	chr4:2866400-2869800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:2866600-2869400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:2866600-2869600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:2866600-2869800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:2866600-2870200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:2866800-2869200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:2866800-2872200	Enhancers	Fetal Heart	heart

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