Variant report

Variant	rs2039951
Chromosome Location	chr13:30494759-30494760
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30482306..30489173-chr13:30491895..30500288,16	MCF-7	breast:
2	chr13:30168413..30170796-chr13:30494094..30496714,3	MCF-7	breast:
3	chr13:30420595..30432624-chr13:30489594..30503683,39	MCF-7	breast:
4	chr13:30494281..30495981-chr13:30514922..30517429,2	MCF-7	breast:
5	chr13:30420962..30426189-chr13:30489163..30500098,34	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122042	Chromatin interaction
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11616970	0.98[ASN][1000 genomes]
rs11617644	0.97[ASN][1000 genomes]
rs11618111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11843877	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17074015	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17074040	0.85[JPT][hapmap]
rs17631508	0.87[ASN][1000 genomes]
rs2027459	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2027460	0.98[ASN][1000 genomes]
rs2031491	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2031492	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2039948	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34444526	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56144866	0.98[ASN][1000 genomes]
rs60031463	0.99[ASN][1000 genomes]
rs61947281	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7994117	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912790	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912791	0.98[ASN][1000 genomes]
rs912792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs927735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9314988	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9508590	0.90[GIH][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2039951	EEF1DP3	cis	parietal	SCAN
rs2039951	FAM123A	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30476800-30497600	Weak transcription	Right Atrium	heart
2	chr13:30491600-30501000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr13:30492400-30494800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:30492400-30497400	Enhancers	Hela-S3	cervix
5	chr13:30492400-30500600	Enhancers	HMEC	breast
6	chr13:30492600-30497400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr13:30492800-30495200	Enhancers	Liver	Liver
8	chr13:30492800-30497400	Enhancers	HepG2	liver
9	chr13:30493000-30496800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:30493000-30497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:30493200-30497600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:30493600-30495600	Weak transcription	HSMMtube	muscle
13	chr13:30493600-30495600	Weak transcription	Osteobl	bone
14	chr13:30493600-30496400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:30493600-30496400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:30493600-30496400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:30493600-30496400	Weak transcription	Placenta	Placenta
18	chr13:30493600-30496400	Weak transcription	NHDF-Ad	bronchial
19	chr13:30493600-30496800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:30493600-30498600	Weak transcription	Gastric	stomach
21	chr13:30493800-30494800	Enhancers	Fetal Intestine Large	intestine
22	chr13:30493800-30495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr13:30493800-30495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr13:30493800-30495600	Enhancers	Fetal Stomach	stomach
25	chr13:30493800-30495600	Weak transcription	HSMM	muscle
26	chr13:30493800-30496200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:30493800-30496400	Weak transcription	Pancreas	Pancrea
28	chr13:30493800-30496400	Weak transcription	NH-A	brain
29	chr13:30493800-30496400	Weak transcription	NHEK	skin
30	chr13:30493800-30496400	Weak transcription	NHLF	lung
31	chr13:30493800-30496800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr13:30494000-30494800	Enhancers	Fetal Intestine Small	intestine
33	chr13:30494000-30495000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr13:30494000-30495400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr13:30494000-30496400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr13:30494200-30495200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr13:30494200-30496400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr13:30494200-30497200	Enhancers	A549	lung
39	chr13:30494200-30501400	Enhancers	Stomach Mucosa	stomach
40	chr13:30494400-30496800	Weak transcription	Esophagus	oesophagus
41	chr13:30494400-30497200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr13:30494400-30497400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr13:30494400-30497600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr13:30494400-30497600	Weak transcription	Rectal Mucosa Donor 29	rectum

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