Variant report

Variant	rs2039948
Chromosome Location	chr13:30494959-30494960
allele	A/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
ENSG00000139514	Chromatin interaction
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11616970	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11617644	0.97[ASN][1000 genomes]
rs11618111	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11843877	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.90[AFR][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[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2027460	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2031491	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2031492	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2039951	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	0.98[ASN][1000 genomes]
rs56144866	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60031463	0.99[ASN][1000 genomes]
rs61947281	0.98[ASN][1000 genomes]
rs7994117	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs912790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs912791	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912792	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs927732	0.84[CEU][hapmap]
rs927735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9314988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9508589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9508590	1.00[CEU][hapmap];0.90[GIH][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]

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

No data

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	chr13:30492400-30497400	Enhancers	Hela-S3	cervix
4	chr13:30492400-30500600	Enhancers	HMEC	breast
5	chr13:30492600-30497400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr13:30492800-30495200	Enhancers	Liver	Liver
7	chr13:30492800-30497400	Enhancers	HepG2	liver
8	chr13:30493000-30496800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:30493000-30497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:30493200-30497600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr13:30493600-30495600	Weak transcription	HSMMtube	muscle
12	chr13:30493600-30495600	Weak transcription	Osteobl	bone
13	chr13:30493600-30496400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr13:30493600-30496400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:30493600-30496400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:30493600-30496400	Weak transcription	Placenta	Placenta
17	chr13:30493600-30496400	Weak transcription	NHDF-Ad	bronchial
18	chr13:30493600-30496800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:30493600-30498600	Weak transcription	Gastric	stomach
20	chr13:30493800-30495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:30493800-30495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:30493800-30495600	Enhancers	Fetal Stomach	stomach
23	chr13:30493800-30495600	Weak transcription	HSMM	muscle
24	chr13:30493800-30496200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:30493800-30496400	Weak transcription	Pancreas	Pancrea
26	chr13:30493800-30496400	Weak transcription	NH-A	brain
27	chr13:30493800-30496400	Weak transcription	NHEK	skin
28	chr13:30493800-30496400	Weak transcription	NHLF	lung
29	chr13:30493800-30496800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr13:30494000-30495000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr13:30494000-30495400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr13:30494000-30496400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:30494200-30495200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr13:30494200-30496400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr13:30494200-30497200	Enhancers	A549	lung
36	chr13:30494200-30501400	Enhancers	Stomach Mucosa	stomach
37	chr13:30494400-30496800	Weak transcription	Esophagus	oesophagus
38	chr13:30494400-30497200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr13:30494400-30497400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:30494400-30497600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr13:30494400-30497600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr13:30494800-30495200	Weak transcription	Fetal Intestine Large	intestine
43	chr13:30494800-30495600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:30494800-30496800	Weak transcription	Fetal Intestine Small	intestine

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