Variant report

Variant	rs58738348
Chromosome Location	chr2:98278845-98278846
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:98277387-98280171	K562	blood:	n/a	n/a
2	POLR2A	chr2:98277968-98281074	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:98278131-98281374	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr2:98278745-98278927	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:98278016-98282070	HepG2	liver:	n/a	n/a
6	CHD1	chr2:98278816-98281671	IMR90	lung:	n/a	chr2:98280105-98280115
7	WRNIP1	chr2:98278648-98280144	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:98278423-98278851	GM12891	blood:	n/a	n/a
9	POLR2A	chr2:98277989-98281149	GM12878	blood:	n/a	n/a
10	MTA3	chr2:98278702-98280226	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:98278795-98281292	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:98278623-98281994	K562	blood:	n/a	n/a
13	POLR2A	chr2:98278714-98281017	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:98278471-98280317	K562	blood:	n/a	n/a
15	POLR2A	chr2:98278788-98280959	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:98278748-98281215	K562	blood:	n/a	n/a
17	POLR2A	chr2:98278844-98280935	GM12891	blood:	n/a	n/a
18	POLR2A	chr2:98278131-98281311	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:98278155-98280984	HepG2	liver:	n/a	n/a
20	MAZ	chr2:98278736-98281497	IMR90	lung:	n/a	chr2:98280224-98280234
21	POLR2A	chr2:98278761-98281086	PFSK-1	brain:	n/a	n/a
22	MXI1	chr2:98278424-98281242	IMR90	lung:	n/a	chr2:98280539-98280548 chr2:98279430-98279439
23	POLR2A	chr2:98278415-98281290	K562	blood:	n/a	n/a
24	BHLHE40	chr2:98278808-98278986	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:98278657-98281071	IMR90	lung:	n/a	n/a
26	POLR2A	chr2:98278773-98281032	Raji	blood:	n/a	n/a
27	POLR2A	chr2:98278802-98281079	HEK293	kidney:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:98278220..98280235-chr2:98364964..98367550,2	K562	blood:
2	chr2:98277235..98279650-chr2:98312622..98314344,2	K562	blood:
3	chr2:98277787..98279697-chr2:98287927..98289913,2	MCF-7	breast:
4	chr2:98278667..98281978-chr2:98283382..98286512,4	K562	blood:
5	chr2:98278665..98281371-chr2:98305087..98308005,4	MCF-7	breast:
6	chr2:98277609..98280060-chr2:98302722..98304227,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACTR1B	TF binding region
LINC01125	TF binding region
ENSG00000228486	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12999616	1.00[ASN][1000 genomes]
rs2071038	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2290123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2309149	1.00[ASN][1000 genomes]
rs2922614	1.00[AMR][1000 genomes]
rs34516173	1.00[ASN][1000 genomes]
rs35958372	1.00[ASN][1000 genomes]
rs4069515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57875000	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58184071	1.00[AMR][1000 genomes]
rs59168350	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59523945	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60753457	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61043662	1.00[AMR][1000 genomes]
rs6542982	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6716208	1.00[AMR][1000 genomes]
rs6727416	1.00[EUR][1000 genomes]
rs6753752	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72493438	1.00[ASN][1000 genomes]
rs72493444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72493445	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942846	1.00[AMR][1000 genomes]
rs72942852	1.00[AMR][1000 genomes]
rs72942859	1.00[AMR][1000 genomes]
rs72942873	1.00[AMR][1000 genomes]
rs72946446	1.00[AMR][1000 genomes]
rs72946451	1.00[AMR][1000 genomes]
rs72947032	1.00[AMR][1000 genomes]
rs72947033	1.00[AMR][1000 genomes]
rs72947062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72949064	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72949085	1.00[AMR][1000 genomes]
rs72949092	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949095	1.00[AMR][1000 genomes]
rs7563002	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582819	1.00[EUR][1000 genomes]
rs7608385	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	nsv431402	chr2:97669032-98281634	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	esv2763630	chr2:97731133-98279050	Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1005846	chr2:97972600-98281634	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv1009263	chr2:98013814-98281634	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98275400-98279200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:98276000-98279400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:98276200-98279200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:98276800-98279000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr2:98277000-98279000	Enhancers	Left Ventricle	heart
6	chr2:98277000-98279000	Enhancers	Ovary	ovary
7	chr2:98277200-98279000	Enhancers	HUVEC	blood vessel
8	chr2:98277400-98279000	Genic enhancers	Fetal Stomach	stomach
9	chr2:98277400-98279000	Enhancers	Right Atrium	heart
10	chr2:98277400-98279400	Weak transcription	Aorta	Aorta
11	chr2:98277600-98279000	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:98277600-98279000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:98277600-98279200	Enhancers	Pancreas	Pancrea
14	chr2:98277600-98279400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr2:98277800-98279000	Enhancers	Primary B cells from cord blood	blood
16	chr2:98277800-98279000	Enhancers	Esophagus	oesophagus
17	chr2:98277800-98279000	Enhancers	Lung	lung
18	chr2:98277800-98279200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:98277800-98279600	Enhancers	Spleen	Spleen
20	chr2:98277800-98279800	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr2:98278000-98279000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:98278000-98279000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:98278000-98279200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:98278000-98279200	Enhancers	Brain Substantia Nigra	brain
25	chr2:98278000-98279200	Enhancers	Fetal Brain Male	brain
26	chr2:98278000-98279800	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr2:98278000-98279800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:98278000-98279800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr2:98278200-98279000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:98278200-98279000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:98278200-98279000	Enhancers	Liver	Liver
32	chr2:98278200-98279000	Enhancers	Fetal Muscle Trunk	muscle
33	chr2:98278200-98279200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:98278200-98279200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:98278200-98279400	Enhancers	Stomach Mucosa	stomach
36	chr2:98278200-98279400	Flanking Active TSS	NHDF-Ad	bronchial
37	chr2:98278200-98280000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr2:98278200-98280000	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr2:98278400-98279000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:98278400-98279000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:98278400-98279000	Enhancers	Fetal Intestine Large	intestine
42	chr2:98278400-98279000	Genic enhancers	Fetal Intestine Small	intestine
43	chr2:98278400-98279000	Genic enhancers	Fetal Thymus	thymus
44	chr2:98278400-98279000	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr2:98278400-98279000	Enhancers	NHEK	skin
46	chr2:98278400-98279200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:98278400-98279200	Enhancers	Fetal Lung	lung
48	chr2:98278400-98279400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:98278400-98279400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:98278400-98279400	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links