Variant report

Variant	rs9828488
Chromosome Location	chr3:52224525-52224526
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	EP300	chr3:52224270-52224537	SK-N-SH_RA	brain:	n/a	chr3:52224449-52224456 chr3:52224337-52224353
2	ELF1	chr3:52224236-52224725	GM12878	blood:	n/a	chr3:52224447-52224456 chr3:52224446-52224457 chr3:52224446-52224457 chr3:52224444-52224457
3	MAZ	chr3:52224517-52224850	K562	blood:	n/a	chr3:52224636-52224646
4	TCF12	chr3:52224015-52225073	SK-N-SH	brain:	n/a	chr3:52224486-52224493 chr3:52224343-52224353 chr3:52224347-52224354
5	NFIC	chr3:52224045-52224994	SK-N-SH	brain:	n/a	n/a
6	HMGN3	chr3:52224324-52224566	K562	blood:	n/a	n/a
7	TCF12	chr3:52224084-52225001	SK-N-SH	brain:	n/a	chr3:52224486-52224493 chr3:52224343-52224353 chr3:52224347-52224354
8	ELF1	chr3:52224306-52224636	K562	blood:	n/a	chr3:52224447-52224456 chr3:52224446-52224457 chr3:52224446-52224457 chr3:52224444-52224457
9	NFIC	chr3:52224129-52224751	SK-N-SH	brain:	n/a	n/a
10	ELF1	chr3:52224345-52224692	K562	blood:	n/a	chr3:52224447-52224456 chr3:52224446-52224457 chr3:52224446-52224457 chr3:52224444-52224457

No.	Distal block	Cell Line	Cell type
1	chr3:52224275..52227049-chr3:52256211..52258351,2	K562	blood:
2	chr3:52014600..52016673-chr3:52222522..52224702,2	K562	blood:
3	chr3:52224034..52226671-chr3:52226883..52229368,2	K562	blood:
4	chr13:107543720..107546383-chr3:52224079..52226911,2	K562	blood:
5	chr3:52223120..52225536-chr3:52227053..52228945,2	MCF-7	breast:

Variant related genes	Relation type
ALDOAP1	TF binding region
ENSG00000242849	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10212380	1.00[EUR][1000 genomes]
rs10212560	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10440116	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs13318570	1.00[AMR][1000 genomes]
rs17052143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28413740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5743834	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9813448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813468	1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813489	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9813653	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821916	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834363	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836166	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842960	1.00[EUR][1000 genomes]
rs9843055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9844178	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863874	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9868332	1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52217400-52224800	Weak transcription	Spleen	Spleen
2	chr3:52217600-52231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52218600-52224800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr3:52218800-52229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:52219400-52225000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr3:52219600-52225200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:52220200-52224600	Weak transcription	Right Ventricle	heart
8	chr3:52220200-52230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:52222000-52225000	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:52222200-52225000	Enhancers	Fetal Intestine Small	intestine
11	chr3:52222200-52225400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:52222200-52225400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:52222200-52225400	Enhancers	Fetal Intestine Large	intestine
14	chr3:52222200-52226200	Enhancers	Placenta	Placenta
15	chr3:52222200-52231600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:52222400-52225400	Enhancers	Stomach Mucosa	stomach
17	chr3:52222800-52225400	Enhancers	Pancreas	Pancrea
18	chr3:52223000-52225800	Enhancers	Duodenum Mucosa	Duodenum
19	chr3:52223000-52227000	Enhancers	Fetal Lung	lung
20	chr3:52223200-52224600	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:52223400-52225000	Enhancers	Brain Germinal Matrix	brain
22	chr3:52223400-52228400	Weak transcription	Fetal Thymus	thymus
23	chr3:52223600-52224600	Weak transcription	HepG2	liver
24	chr3:52223600-52225400	Enhancers	Gastric	stomach
25	chr3:52223600-52226000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:52223600-52227000	Enhancers	Fetal Muscle Trunk	muscle
27	chr3:52223800-52224800	Enhancers	Brain Anterior Caudate	brain
28	chr3:52223800-52225000	Enhancers	Esophagus	oesophagus
29	chr3:52223800-52225200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52223800-52225200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:52223800-52225400	Enhancers	Colonic Mucosa	Colon
32	chr3:52223800-52225400	Enhancers	Osteobl	bone
33	chr3:52223800-52226000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:52223800-52226200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:52223800-52227800	Enhancers	Fetal Muscle Leg	muscle
36	chr3:52224000-52224800	Enhancers	Aorta	Aorta
37	chr3:52224000-52225000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:52224000-52225000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:52224000-52225000	Enhancers	Colon Smooth Muscle	Colon
40	chr3:52224000-52225000	Enhancers	HMEC	breast
41	chr3:52224000-52225000	Enhancers	HSMMtube	muscle
42	chr3:52224000-52225200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:52224000-52225400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:52224000-52225400	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:52224000-52225400	Enhancers	HSMM	muscle
46	chr3:52224000-52226000	Enhancers	Fetal Stomach	stomach
47	chr3:52224000-52230000	Enhancers	Ovary	ovary
48	chr3:52224200-52224600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:52224200-52224600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:52224200-52224600	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links