Variant report

Variant	rs13123779
Chromosome Location	chr4:3013035-3013036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2938205..2940461-chr4:3011705..3013436,2	MCF-7	breast:
2	chr4:2963576..2965499-chr4:3012277..3014401,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12506119	0.80[ASN][1000 genomes]
rs12512648	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12696706	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13103004	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13104559	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13104987	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13109886	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111777	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13132131	0.82[EUR][1000 genomes]
rs1419043	0.95[ASN][1000 genomes]
rs1978031	0.91[ASN][1000 genomes]
rs1978032	0.91[ASN][1000 genomes]
rs34020100	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34163500	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34540265	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35163447	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35781129	0.98[ASN][1000 genomes]
rs35909590	0.98[ASN][1000 genomes]
rs60504719	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60635068	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6856669	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1008527	chr4:2957814-3019042	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv878453	chr4:2963222-3021383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008781	chr4:2964080-3019042	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv870141	chr4:2982146-3021346	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2979600-3025000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:2983600-3032000	Weak transcription	Fetal Brain Female	brain
3	chr4:2991400-3024600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:3003800-3024600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:3005000-3018600	Weak transcription	Left Ventricle	heart
6	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
7	chr4:3007000-3020600	Weak transcription	Brain Germinal Matrix	brain
8	chr4:3007200-3015200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:3007600-3024600	Weak transcription	Brain Angular Gyrus	brain
10	chr4:3008000-3013200	Weak transcription	Esophagus	oesophagus
11	chr4:3010600-3013400	Enhancers	HMEC	breast
12	chr4:3010800-3013200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:3011200-3013400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:3011200-3013800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:3011200-3013800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:3011200-3013800	Enhancers	Hela-S3	cervix
17	chr4:3011200-3014400	Enhancers	Stomach Mucosa	stomach
18	chr4:3011600-3013800	Enhancers	Fetal Lung	lung
19	chr4:3011800-3013400	Enhancers	NHEK	skin
20	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
21	chr4:3012000-3013200	Weak transcription	Gastric	stomach
22	chr4:3012200-3013600	Enhancers	Osteobl	bone
23	chr4:3012200-3013800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:3012200-3013800	Enhancers	NHLF	lung
25	chr4:3012400-3013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:3012400-3013600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:3012400-3013800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:3012400-3013800	Enhancers	Adipose Nuclei	Adipose
29	chr4:3012400-3013800	Enhancers	Placenta	Placenta
30	chr4:3012400-3013800	Enhancers	Pancreas	Pancrea
31	chr4:3012400-3013800	Enhancers	HSMM	muscle
32	chr4:3012600-3015000	Weak transcription	GM12878-XiMat	blood
33	chr4:3012800-3013400	Weak transcription	Fetal Intestine Large	intestine
34	chr4:3012800-3013600	Enhancers	Fetal Intestine Small	intestine
35	chr4:3012800-3013800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:3012800-3013800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:3012800-3013800	Enhancers	NHDF-Ad	bronchial
38	chr4:3012800-3024800	Weak transcription	Aorta	Aorta
39	chr4:3013000-3013200	Enhancers	Ovary	ovary
40	chr4:3013000-3013400	Weak transcription	HSMMtube	muscle
41	chr4:3013000-3013800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links