Variant report

Variant	rs2133575
Chromosome Location	chr3:98616861-98616862
allele	A/C
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	chr3:98598356-98618077	U87	brain:	n/a	n/a
2	POLR2A	chr3:98601861-98618157	U87	brain:	n/a	n/a
3	POLR2A	chr3:98601867-98618131	U87	brain:	n/a	n/a
4	POLR2A	chr3:98592632-98618071	U87	brain:	n/a	n/a
5	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:98616122..98617678-chr3:98626780..98628544,2	MCF-7	breast:
2	chr3:98615054..98618037-chr3:98618914..98621947,4	MCF-7	breast:
3	chr3:98612040..98614381-chr3:98615644..98617594,2	MCF-7	breast:

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000239462	TF binding region
ENSG00000057019	Chromatin interaction
ENSG00000207331	Chromatin interaction
ENSG00000239462	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10935512	0.86[AFR][1000 genomes]
rs12330381	0.87[ASN][1000 genomes]
rs13094707	0.87[ASN][1000 genomes]
rs13318536	0.87[ASN][1000 genomes]
rs13318960	0.80[ASN][1000 genomes]
rs13327449	0.80[ASN][1000 genomes]
rs13327485	0.80[ASN][1000 genomes]
rs1351496	0.95[AFR][1000 genomes]
rs1383908	0.98[AFR][1000 genomes]
rs1440157	0.98[AFR][1000 genomes]
rs1531736	0.95[AFR][1000 genomes]
rs1600788	0.97[AFR][1000 genomes]
rs1818053	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1972432	0.95[AFR][1000 genomes]
rs2128053	0.98[AFR][1000 genomes]
rs2173598	0.98[AFR][1000 genomes]
rs2439230	0.86[AFR][1000 genomes]
rs2439234	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2439235	0.86[AFR][1000 genomes]
rs2448985	0.84[AFR][1000 genomes]
rs2454672	0.94[AFR][1000 genomes]
rs2454681	0.95[AFR][1000 genomes]
rs2454683	0.98[AFR][1000 genomes]
rs2454687	1.00[ASN][1000 genomes]
rs2454690	0.85[AFR][1000 genomes]
rs2470820	0.82[AFR][1000 genomes]
rs2470828	0.81[AFR][1000 genomes]
rs2470839	0.82[AFR][1000 genomes]
rs2470856	0.95[AFR][1000 genomes]
rs2470858	0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2470866	0.85[AFR][1000 genomes]
rs2470868	0.98[AFR][1000 genomes]
rs2470874	0.88[AFR][1000 genomes]
rs2470883	0.98[AFR][1000 genomes]
rs2470884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528154	0.80[ASN][1000 genomes]
rs28637457	0.87[ASN][1000 genomes]
rs28650813	0.80[ASN][1000 genomes]
rs28821579	0.87[ASN][1000 genomes]
rs28883308	0.80[ASN][1000 genomes]
rs2929491	0.82[AFR][1000 genomes]
rs34693680	0.87[ASN][1000 genomes]
rs4273318	0.98[AFR][1000 genomes]
rs4857107	0.92[AFR][1000 genomes]
rs5013928	0.98[AFR][1000 genomes]
rs6795351	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7373983	0.84[AFR][1000 genomes]
rs7621508	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626395	0.88[AFR][1000 genomes]
rs7630797	0.92[AFR][1000 genomes]
rs828611	1.00[AMR][1000 genomes]
rs828622	0.81[AFR][1000 genomes]
rs866873	0.81[AFR][1000 genomes]
rs9289696	0.87[ASN][1000 genomes]
rs9289700	0.87[ASN][1000 genomes]
rs9819279	0.87[ASN][1000 genomes]
rs9819309	0.87[ASN][1000 genomes]
rs9828045	0.87[ASN][1000 genomes]
rs9842226	0.87[ASN][1000 genomes]
rs9848335	0.87[ASN][1000 genomes]
rs9850469	0.87[ASN][1000 genomes]
rs9852889	0.87[ASN][1000 genomes]
rs9859042	0.87[ASN][1000 genomes]
rs9864010	0.87[ASN][1000 genomes]
rs9872073	0.80[ASN][1000 genomes]
rs9872301	0.80[ASN][1000 genomes]
rs9879302	0.87[ASN][1000 genomes]
rs996199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
4	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
6	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
7	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
8	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:98610800-98618400	Weak transcription	Brain Anterior Caudate	brain
10	chr3:98610800-98618400	Enhancers	Fetal Heart	heart
11	chr3:98610800-98618600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:98611200-98617000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:98611400-98618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:98611400-98619200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:98611800-98618400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:98611800-98618600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:98612000-98618800	Weak transcription	Psoas Muscle	Psoas
18	chr3:98612600-98618400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:98612800-98617400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:98612800-98618400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:98613000-98617600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:98613000-98618400	Weak transcription	GM12878-XiMat	blood
23	chr3:98613000-98618600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:98613000-98618600	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:98613000-98618600	Weak transcription	HSMMtube	muscle
26	chr3:98613200-98618600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:98613200-98618800	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:98613200-98619200	Weak transcription	Aorta	Aorta
29	chr3:98613200-98619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:98613400-98617200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:98613400-98618400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:98613600-98617200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:98613600-98617800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:98613600-98618000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:98613600-98618200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:98613600-98619400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:98614200-98617400	Weak transcription	Right Ventricle	heart
38	chr3:98614200-98619600	Weak transcription	Gastric	stomach
39	chr3:98614400-98618400	Weak transcription	Brain Germinal Matrix	brain
40	chr3:98614400-98618400	Weak transcription	Right Atrium	heart
41	chr3:98614400-98618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:98614400-98619000	Weak transcription	K562	blood
43	chr3:98614600-98618400	Weak transcription	Ovary	ovary
44	chr3:98615000-98618200	Weak transcription	Left Ventricle	heart
45	chr3:98615000-98618400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:98615000-98619400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:98615000-98620400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:98615200-98618600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:98615600-98619600	Flanking Active TSS	HUVEC	blood vessel
50	chr3:98615600-98621200	Active TSS	NHLF	lung

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