Variant report

Variant	rs2454672
Chromosome Location	chr3:98621898-98621899
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	POLR2A	chr3:98621871-98622309	HCT-116	colon:	n/a	n/a
2	POLR2A	chr3:98618257-98622361	U87	brain:	n/a	n/a
3	POLR2A	chr3:98618299-98622361	U87	brain:	n/a	n/a
4	POLR2A	chr3:98618148-98622423	U87	brain:	n/a	n/a
5	POLR2A	chr3:98618120-98622417	U87	brain:	n/a	n/a
6	CHD1	chr3:98618292-98622396	IMR90	lung:	n/a	chr3:98620361-98620371
7	TCF12	chr3:98618229-98622320	A549	lung:	n/a	n/a
8	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a
9	GATA3	chr3:98621678-98622355	A549	lung:	n/a	n/a
10	POLR2A	chr3:98621752-98622223	SK-N-SH	brain:	n/a	n/a
11	SP1	chr3:98621689-98622458	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98620298..98622928-chr3:98626076..98627807,2	MCF-7	breast:

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000207331	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383908	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1600788	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1818053	0.81[AFR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2133575	0.94[AFR][1000 genomes]
rs2173598	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2448985	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470828	1.00[AMR][1000 genomes]
rs2470839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	1.00[AMR][1000 genomes]
rs2470856	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470883	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470884	0.94[AFR][1000 genomes]
rs278375	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4273318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5013928	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs6795351	0.91[AFR][1000 genomes]
rs7373983	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626395	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][1000 genomes]
rs996199	0.94[AFR][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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98617400-98622000	Active TSS	Right Ventricle	heart
2	chr3:98618800-98622200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:98621000-98622000	Flanking Active TSS	NH-A	brain
4	chr3:98621000-98622200	Flanking Active TSS	NHEK	skin
5	chr3:98621200-98622000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:98621200-98622000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:98621200-98622200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:98621200-98622400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:98621200-98622400	Flanking Active TSS	A549	lung
10	chr3:98621200-98622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:98621400-98622000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:98621400-98622000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:98621400-98622200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:98621400-98622200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:98621400-98622200	Enhancers	HSMM	muscle
16	chr3:98621400-98622600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:98621400-98625000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:98621600-98622000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:98621600-98622000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:98621600-98622000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:98621600-98622000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:98621600-98622000	Enhancers	Colon Smooth Muscle	Colon
23	chr3:98621600-98622000	Enhancers	Thymus	Thymus
24	chr3:98621600-98622000	Enhancers	HepG2	liver
25	chr3:98621600-98622200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:98621600-98622200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:98621600-98622200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:98621600-98622200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:98621600-98622200	Enhancers	Fetal Lung	lung
30	chr3:98621600-98622200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:98621600-98622200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:98621600-98622200	Enhancers	HMEC	breast
33	chr3:98621600-98622400	Enhancers	Osteobl	bone
34	chr3:98621600-98625000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr3:98621600-98625200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:98621600-98625400	Weak transcription	Psoas Muscle	Psoas
37	chr3:98621800-98622000	Enhancers	Brain Angular Gyrus	brain
38	chr3:98621800-98622000	Enhancers	Fetal Brain Female	brain
39	chr3:98621800-98622200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr3:98621800-98622200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr3:98621800-98622200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr3:98621800-98622200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr3:98621800-98622200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:98621800-98622200	Enhancers	Fetal Heart	heart
45	chr3:98621800-98622200	Enhancers	Rectal Smooth Muscle	rectum
46	chr3:98621800-98622200	Enhancers	Dnd41	blood
47	chr3:98621800-98622200	Enhancers	NHLF	lung
48	chr3:98621800-98622400	Enhancers	Brain Germinal Matrix	brain
49	chr3:98621800-98622400	Weak transcription	GM12878-XiMat	blood
50	chr3:98621800-98623000	Weak transcription	HUVEC	blood vessel

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