Variant report

Variant	rs278381
Chromosome Location	chr3:98528262-98528263
allele	A/G
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	chr3:98523635-98529478	U87	brain:	n/a	n/a
2	POLR2A	chr3:98523592-98529440	U87	brain:	n/a	n/a
3	POLR2A	chr3:98523586-98529440	U87	brain:	n/a	n/a
4	RUNX3	chr3:98528133-98528773	GM12878	blood:	n/a	n/a
5	NFIC	chr3:98528113-98528890	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:98523621-98529478	U87	brain:	n/a	n/a
7	EBF1	chr3:98528220-98528733	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:98528243-98528457	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98310981..98313806-chr3:98526146..98529080,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-26P	TF binding region
ENSG00000080819	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10935514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1095911	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632798	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12636683	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13071075	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13316760	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1371687	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2333923	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2439237	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs278376	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs278379	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278382	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278387	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278390	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35483904	0.81[EUR][1000 genomes]
rs4577404	0.82[EUR][1000 genomes]
rs4857415	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767370	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6774875	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6791389	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7615628	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7615856	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs828603	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs828605	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs828610	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs828614	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs828616	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828617	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs828618	0.84[CEU][hapmap]
rs828621	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs852701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8833	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs955351	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs278381	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx
rs278381	DCBLD2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98503400-98576400	Weak transcription	Gastric	stomach
3	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
4	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
7	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
8	chr3:98516800-98528600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
10	chr3:98517200-98531400	Weak transcription	Hela-S3	cervix
11	chr3:98522400-98533800	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr3:98523400-98531400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:98523600-98528600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:98523600-98533800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:98523600-98535200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:98523800-98528400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:98523800-98528400	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:98523800-98529200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:98523800-98529200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr3:98523800-98529200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr3:98523800-98529400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:98523800-98529400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:98523800-98529600	Strong transcription	Fetal Lung	lung
24	chr3:98523800-98530000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:98523800-98530200	Strong transcription	Dnd41	blood
26	chr3:98523800-98530400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr3:98523800-98530400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:98523800-98530600	Strong transcription	HUVEC	blood vessel
29	chr3:98523800-98531400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:98523800-98531400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:98523800-98533600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:98523800-98533600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:98523800-98533800	Strong transcription	NHDF-Ad	bronchial
34	chr3:98523800-98535000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:98524200-98530400	Strong transcription	NHLF	lung
38	chr3:98524200-98544200	Strong transcription	HSMM	muscle
39	chr3:98524400-98528600	Strong transcription	HepG2	liver
40	chr3:98524800-98530400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:98525400-98529200	Genic enhancers	NH-A	brain
42	chr3:98525600-98528400	Genic enhancers	HMEC	breast
43	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
44	chr3:98526000-98528600	Genic enhancers	NHEK	skin
45	chr3:98526200-98543200	Weak transcription	Lung	lung
46	chr3:98526400-98528400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:98526400-98528400	Weak transcription	Thymus	Thymus
48	chr3:98526400-98528600	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:98526400-98529200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:98526400-98532000	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links