Variant report

Variant	rs17833250
Chromosome Location	chr4:2870745-2870746
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2868702..2870783-chr4:2881589..2883580,3	K562	blood:
2	chr2:226959307..226961604-chr4:2869808..2871481,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10026792	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014947	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs1034400	1.00[CHB][hapmap]
rs12623	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1263412	0.83[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12641947	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs16843596	1.00[CHB][hapmap]
rs16843603	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17833172	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[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];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs1877723	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2032470	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2096760	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs41528047	1.00[CHB][hapmap]
rs4690006	1.00[CHB][hapmap]
rs55927173	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58115360	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59150074	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624833	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs6600769	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819310	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6824567	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7655104	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7678161	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs17833250	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs17833250	NOP14	cis	cerebellum	SCAN
rs17833250	STX18	cis	parietal	SCAN
rs17833250	LRPAP1	cis	parietal	SCAN
rs17833250	TETRAN	cis	multi-tissue	Pritchard
rs17833250	ADD1	cis	multi-tissue	Pritchard
rs17833250	RNF4	cis	cerebellum	SCAN
rs17833250	GRK4	cis	Artery Tibial	GTEx
rs17833250	CYTL1	cis	parietal	SCAN
rs17833250	GRK4	cis	cerebellum	SCAN
rs17833250	LRPAP1	cis	cerebellum	SCAN
rs17833250	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	chr4:2857400-2877600	Weak transcription	HMEC	breast
3	chr4:2860800-2871000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:2861400-2872600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:2864600-2877400	Weak transcription	NHEK	skin
6	chr4:2864800-2873200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:2865600-2871200	Enhancers	Primary hematopoietic stem cells	blood
8	chr4:2865600-2871400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:2866200-2872400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:2866800-2872200	Enhancers	Fetal Heart	heart
11	chr4:2867400-2871400	Weak transcription	A549	lung
12	chr4:2867400-2873200	Weak transcription	GM12878-XiMat	blood
13	chr4:2867800-2871000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr4:2868000-2871600	Enhancers	Brain Germinal Matrix	brain
15	chr4:2868200-2871600	Enhancers	Small Intestine	intestine
16	chr4:2868400-2871400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr4:2868400-2872600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:2868400-2872600	Enhancers	Fetal Intestine Large	intestine
19	chr4:2868600-2871200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:2868600-2871200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:2868600-2871400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr4:2868800-2870800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr4:2868800-2870800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:2868800-2872000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr4:2869000-2871000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr4:2869000-2871200	Enhancers	H9 Cell Line	embryonic stem cell
27	chr4:2869000-2872200	Genic enhancers	Primary B cells from peripheral blood	blood
28	chr4:2869200-2870800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:2869200-2871000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:2869200-2871200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:2869200-2872600	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr4:2869400-2870800	Flanking Active TSS	Right Atrium	heart
33	chr4:2869400-2871200	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr4:2869400-2871200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr4:2869400-2871200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr4:2869400-2871400	Enhancers	Colonic Mucosa	Colon
37	chr4:2869600-2870800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:2869600-2871200	Enhancers	Lung	lung
39	chr4:2869600-2871200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:2869600-2871600	Active TSS	Brain Angular Gyrus	brain
41	chr4:2869600-2871600	Enhancers	Pancreas	Pancrea
42	chr4:2869600-2871800	Flanking Active TSS	Left Ventricle	heart
43	chr4:2869600-2872000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:2869600-2873000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr4:2869800-2870800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:2869800-2871200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:2869800-2871200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:2869800-2871200	Strong transcription	Thymus	Thymus
49	chr4:2869800-2871400	Enhancers	Gastric	stomach
50	chr4:2869800-2871600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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