Variant report

Variant	rs13319666
Chromosome Location	chr3:98615924-98615925
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	chr3:98598356-98618077	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	chr3:98615562-98615942	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:98592632-98618071	U87	brain:	n/a	n/a
6	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a

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

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

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10935513	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935514	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12632798	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12636683	0.83[AMR][1000 genomes]
rs12695786	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13071075	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13081543	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13316760	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1371687	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1383906	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1383907	0.83[EUR][1000 genomes]
rs2062058	0.84[ASN][1000 genomes]
rs2333923	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2340794	0.80[EUR][1000 genomes]
rs2439237	0.82[ASN][1000 genomes]
rs2449046	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2470853	0.84[ASN][1000 genomes]
rs2470855	0.84[ASN][1000 genomes]
rs2470870	0.84[ASN][1000 genomes]
rs2470872	0.85[ASN][1000 genomes]
rs2470873	0.83[EUR][1000 genomes]
rs2470877	0.83[EUR][1000 genomes]
rs2470880	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs278379	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35483904	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35760367	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35936923	0.83[EUR][1000 genomes]
rs4546099	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577404	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4857415	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6767370	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6774875	0.84[ASN][1000 genomes]
rs6791389	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7615628	0.84[ASN][1000 genomes]
rs7615856	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828614	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs828617	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs828621	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs870202	0.84[ASN][1000 genomes]
rs955351	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9682876	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837206	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9842522	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9880179	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13319666	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx
rs13319666	DCBLD2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
3	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
5	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
7	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
8	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
9	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:98610400-98616600	Transcr. at gene 5' and 3'	A549	lung
11	chr3:98610800-98618400	Weak transcription	Brain Anterior Caudate	brain
12	chr3:98610800-98618400	Enhancers	Fetal Heart	heart
13	chr3:98610800-98618600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:98611200-98617000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:98611400-98618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:98611400-98619200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:98611600-98616600	Weak transcription	Fetal Lung	lung
18	chr3:98611800-98618400	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:98611800-98618600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:98612000-98618800	Weak transcription	Psoas Muscle	Psoas
21	chr3:98612600-98616000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:98612600-98616000	Transcr. at gene 5' and 3'	HMEC	breast
23	chr3:98612600-98618400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:98612800-98617400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:98612800-98618400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:98613000-98616000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:98613000-98616200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
28	chr3:98613000-98617600	Weak transcription	Adipose Nuclei	Adipose
29	chr3:98613000-98618400	Weak transcription	GM12878-XiMat	blood
30	chr3:98613000-98618600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:98613000-98618600	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:98613000-98618600	Weak transcription	HSMMtube	muscle
33	chr3:98613200-98616000	Weak transcription	HepG2	liver
34	chr3:98613200-98616200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:98613200-98616200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:98613200-98618600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:98613200-98618800	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:98613200-98619200	Weak transcription	Aorta	Aorta
39	chr3:98613200-98619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:98613400-98616600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:98613400-98616600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:98613400-98617200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:98613400-98618400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:98613600-98616000	Weak transcription	HSMM	muscle
45	chr3:98613600-98616200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:98613600-98616400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:98613600-98616800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:98613600-98617200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:98613600-98617800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:98613600-98618000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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