Variant report

Variant	rs16843773
Chromosome Location	chr4:3042258-3042259
allele	C/T
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	SPI1	chr4:3042098-3042470	GM12891	blood:	n/a	n/a
2	MTA3	chr4:3042029-3044138	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:3042210-3043957	GM18526	blood:	n/a	n/a
4	POLR2A	chr4:3042151-3043922	GM12892	blood:	n/a	n/a
5	POLR2A	chr4:3042178-3044027	GM12892	blood:	n/a	n/a
6	ZNF143	chr4:3042205-3042405	GM12878	blood:	n/a	n/a
7	MXI1	chr4:3042207-3042555	GM12878	blood:	n/a	n/a
8	EBF1	chr4:3042143-3043940	GM12878	blood:	n/a	chr4:3043105-3043116
9	RUNX3	chr4:3041924-3043896	GM12878	blood:	n/a	n/a
10	ELF1	chr4:3042075-3042729	GM12878	blood:	n/a	chr4:3042273-3042285
11	RUNX3	chr4:3041863-3044165	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:3042215-3043929	GM18951	blood:	n/a	n/a
13	SPI1	chr4:3042208-3042442	GM12878	blood:	n/a	n/a
14	SPI1	chr4:3041954-3042730	GM12878	blood:	n/a	n/a
15	EP300	chr4:3042233-3042694	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:3041640-3044734	GM12891	blood:	n/a	n/a
17	ZEB1	chr4:3042175-3042444	GM12878	blood:	n/a	n/a
18	FOXM1	chr4:3042146-3043263	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:3042157-3044616	GM12878	blood:	n/a	n/a
20	PAX5	chr4:3042120-3043907	GM12878	blood:	n/a	chr4:3042244-3042253
21	POLR2A	chr4:3042135-3044075	GM12878	blood:	n/a	n/a
22	STAT5A	chr4:3042193-3043181	GM12878	blood:	n/a	chr4:3042796-3042808 chr4:3042244-3042255
23	POLR2A	chr4:3042204-3043918	GM10847	blood:	n/a	n/a
24	POLR2A	chr4:3042124-3044657	GM18505	blood:	n/a	n/a
25	SP1	chr4:3042186-3042795	GM12878	blood:	n/a	n/a
26	NFATC1	chr4:3042215-3042835	GM12878	blood:	n/a	n/a
27	NFIC	chr4:3042196-3042844	GM12878	blood:	n/a	n/a
28	RCOR1	chr4:3042248-3042707	GM12878	blood:	n/a	n/a
29	BHLHE40	chr4:3042034-3044019	GM12878	blood:	n/a	chr4:3043518-3043534 chr4:3043900-3043916 chr4:3043010-3043026
30	POLR2A	chr4:3042188-3042626	GM12891	blood:	n/a	n/a
31	POLR2A	chr4:3042113-3042525	GM12891	blood:	n/a	n/a
32	POU2F2	chr4:3042167-3042808	GM12891	blood:	n/a	n/a
33	CHD1	chr4:3042158-3043826	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:3042193-3044036	GM12892	blood:	n/a	n/a
35	ELF1	chr4:3042019-3044065	GM12878	blood:	n/a	chr4:3042273-3042285
36	POLR2A	chr4:3042197-3042546	GM12891	blood:	n/a	n/a
37	MTA3	chr4:3042156-3043414	GM12878	blood:	n/a	n/a
38	EBF1	chr4:3042201-3042893	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:3042174-3043956	GM12891	blood:	n/a	n/a
40	POLR2A	chr4:3042202-3042597	GM12892	blood:	n/a	n/a
41	SPI1	chr4:3042195-3042484	GM12878	blood:	n/a	n/a
42	MAX	chr4:3042171-3043968	GM12878	blood:	n/a	chr4:3043238-3043246
43	YY1	chr4:3042172-3042424	GM12891	blood:	n/a	n/a
44	POLR2A	chr4:3042171-3044373	GM19193	blood:	n/a	n/a
45	BCLAF1	chr4:3042197-3042628	GM12878	blood:	n/a	chr4:3042244-3042253
46	POLR2A	chr4:3042121-3044005	GM15510	blood:	n/a	n/a
47	POLR2A	chr4:3042169-3042585	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:3042176-3042455	GM12878	blood:	n/a	n/a
49	RELA	chr4:3042188-3044252	GM15510	blood:	n/a	n/a
50	NFIC	chr4:3041854-3043903	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-204P	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11929714	0.87[EUR][1000 genomes]
rs1936032	1.00[CEU][hapmap]
rs2105380	0.82[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs34857805	0.87[EUR][1000 genomes]
rs55646607	0.84[EUR][1000 genomes]
rs55942209	0.82[EUR][1000 genomes]
rs56340718	0.87[EUR][1000 genomes]
rs58892460	0.87[EUR][1000 genomes]
rs60003208	0.84[EUR][1000 genomes]
rs61293276	1.00[EUR][1000 genomes]
rs61321259	1.00[EUR][1000 genomes]
rs61487059	0.87[EUR][1000 genomes]
rs6812304	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6815398	1.00[EUR][1000 genomes]
rs6824519	1.00[EUR][1000 genomes]
rs6834166	0.83[EUR][1000 genomes]
rs6837436	0.87[EUR][1000 genomes]
rs6843832	0.83[EUR][1000 genomes]
rs6846128	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs6848638	1.00[EUR][1000 genomes]
rs6853929	1.00[EUR][1000 genomes]
rs6854307	0.87[EUR][1000 genomes]
rs73084109	0.87[EUR][1000 genomes]
rs73084117	0.87[EUR][1000 genomes]
rs73084128	0.87[EUR][1000 genomes]
rs73086111	1.00[EUR][1000 genomes]
rs73086113	1.00[EUR][1000 genomes]
rs73086116	0.91[EUR][1000 genomes]
rs73792175	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7657057	0.91[EUR][1000 genomes]
rs7677445	0.83[TSI][hapmap]

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	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16843773	ADAM23	trans	lymphoblastoid	seeQTL
rs16843773	GRK4	cis	lymphoblastoid	seeQTL
rs16843773	GRK4	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
2	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
3	chr4:3025600-3042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:3025600-3042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:3032400-3042400	Weak transcription	Fetal Brain Female	brain
6	chr4:3038400-3042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:3039400-3042800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:3039400-3043000	Weak transcription	Pancreas	Pancrea
9	chr4:3039600-3042800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:3039800-3043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:3039800-3043000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:3039800-3043200	Weak transcription	Fetal Kidney	kidney
13	chr4:3040000-3042400	Weak transcription	Spleen	Spleen
14	chr4:3040000-3042600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:3040000-3043000	Weak transcription	Psoas Muscle	Psoas
16	chr4:3040000-3043000	Weak transcription	Right Atrium	heart
17	chr4:3040200-3042400	Weak transcription	Colonic Mucosa	Colon
18	chr4:3040200-3042400	Weak transcription	Placenta	Placenta
19	chr4:3040200-3042600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:3040200-3042800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:3040200-3042800	Weak transcription	Liver	Liver
22	chr4:3040200-3042800	Weak transcription	Brain Anterior Caudate	brain
23	chr4:3040200-3042800	Weak transcription	NHLF	lung
24	chr4:3040200-3043000	Weak transcription	Brain Substantia Nigra	brain
25	chr4:3040200-3043000	Weak transcription	Right Ventricle	heart
26	chr4:3040200-3043200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:3040400-3042400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:3040400-3042600	Weak transcription	Adipose Nuclei	Adipose
29	chr4:3040400-3042800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:3040400-3042800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:3040400-3042800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:3040400-3042800	Weak transcription	Osteobl	bone
33	chr4:3040600-3042400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr4:3040600-3042400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:3040600-3042400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:3040600-3042400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:3040600-3042400	Weak transcription	NHDF-Ad	bronchial
38	chr4:3040600-3042600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:3040600-3042600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:3040600-3042600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:3040600-3042600	Weak transcription	Esophagus	oesophagus
42	chr4:3040600-3042600	Weak transcription	Lung	lung
43	chr4:3040600-3042600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:3040600-3042600	Weak transcription	HSMM	muscle
45	chr4:3040600-3042800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:3040600-3042800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:3040600-3042800	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:3040600-3042800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:3040600-3042800	Weak transcription	Fetal Heart	heart
50	chr4:3040600-3042800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links