Variant report

Variant	rs3021124
Chromosome Location	chr4:3040012-3040013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3038856..3040749-chr4:3043216..3045055,2	MCF-7	breast:
2	chr4:2963384..2966689-chr4:3039150..3042099,3	MCF-7	breast:
3	chr4:3038898..3040591-chr4:3042630..3044225,2	K562	blood:
4	chr4:3023335..3025840-chr4:3038489..3040216,2	K562	blood:
5	chr4:2962324..2965157-chr4:3038658..3041548,2	K562	blood:

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10010375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2471343	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2471348	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2488811	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2515934	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2515955	0.89[EUR][1000 genomes]
rs2515956	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28795684	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28856696	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2960299	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2995802	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs61269488	0.84[AMR][1000 genomes];0.89[EUR][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	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

No data

Chromatin state (count:88 , 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	chr4:3038200-3040800	Enhancers	Fetal Muscle Trunk	muscle
7	chr4:3038400-3040200	Enhancers	Fetal Intestine Small	intestine
8	chr4:3038400-3042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:3038600-3040200	Enhancers	Colonic Mucosa	Colon
10	chr4:3038600-3040200	Enhancers	Right Ventricle	heart
11	chr4:3038600-3040600	Enhancers	Fetal Heart	heart
12	chr4:3038600-3040600	Enhancers	Gastric	stomach
13	chr4:3038600-3042200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:3038800-3040200	Enhancers	Liver	Liver
15	chr4:3038800-3040200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr4:3038800-3040200	Enhancers	Placenta	Placenta
17	chr4:3038800-3040600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr4:3038800-3040600	Enhancers	NHDF-Ad	bronchial
19	chr4:3038800-3041000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:3039000-3040200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr4:3039000-3040200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr4:3039000-3040200	Enhancers	Stomach Mucosa	stomach
23	chr4:3039000-3040400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr4:3039000-3040400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:3039000-3040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:3039000-3040600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:3039000-3040600	Enhancers	Esophagus	oesophagus
28	chr4:3039000-3040600	Enhancers	Left Ventricle	heart
29	chr4:3039000-3040600	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr4:3039000-3040600	Enhancers	HSMMtube	muscle
31	chr4:3039200-3040200	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr4:3039200-3040200	Active TSS	Brain Anterior Caudate	brain
33	chr4:3039200-3040400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr4:3039200-3040400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr4:3039200-3040400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr4:3039200-3040400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr4:3039200-3040600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:3039200-3040600	Enhancers	HSMM	muscle
39	chr4:3039400-3040200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr4:3039400-3040600	Enhancers	Fetal Lung	lung
41	chr4:3039400-3042800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr4:3039400-3043000	Weak transcription	Pancreas	Pancrea
43	chr4:3039600-3040200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr4:3039600-3040200	Flanking Active TSS	NHLF	lung
45	chr4:3039600-3040400	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr4:3039600-3040400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr4:3039600-3040400	Flanking Active TSS	HepG2	liver
48	chr4:3039600-3040600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr4:3039600-3040600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr4:3039600-3040600	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links