Variant report

Variant	rs72979962
Chromosome Location	chr3:53838352-53838353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53826568..53829356-chr3:53836868..53838582,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13319223	1.00[AMR][1000 genomes]
rs13353529	1.00[AMR][1000 genomes]
rs58288602	1.00[AMR][1000 genomes]
rs72977420	1.00[AMR][1000 genomes]
rs72982040	1.00[AMR][1000 genomes]
rs72982042	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982043	1.00[AMR][1000 genomes]
rs72982055	1.00[AMR][1000 genomes]
rs893368	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9311515	1.00[AMR][1000 genomes]
rs9654000	1.00[AMR][1000 genomes]
rs9849534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9858883	1.00[AMR][1000 genomes]
rs9863776	1.00[AMR][1000 genomes]
rs9864070	1.00[AMR][1000 genomes]
rs9869730	1.00[AMR][1000 genomes]
rs9880201	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1002375	chr3:53822319-53872753	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	esv3437902	chr3:53837712-53842010	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53811400-53838600	Weak transcription	Spleen	Spleen
2	chr3:53811600-53843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:53829200-53853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:53830400-53839800	Weak transcription	Lung	lung
5	chr3:53830400-53851200	Weak transcription	Fetal Brain Male	brain
6	chr3:53830600-53838600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:53830600-53838600	Weak transcription	Fetal Brain Female	brain
8	chr3:53830600-53840200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:53830600-53840200	Weak transcription	Pancreas	Pancrea
10	chr3:53830800-53838800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:53830800-53840200	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:53832000-53839800	Strong transcription	Fetal Intestine Large	intestine
13	chr3:53832200-53838800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:53832200-53839800	Strong transcription	Fetal Intestine Small	intestine
15	chr3:53833000-53838400	Weak transcription	Fetal Heart	heart
16	chr3:53833600-53838400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:53833600-53840800	Weak transcription	Fetal Kidney	kidney
18	chr3:53834400-53838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:53834600-53838600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:53834800-53838400	Weak transcription	HSMMtube	muscle
21	chr3:53837400-53839000	Weak transcription	Fetal Lung	lung
22	chr3:53837400-53839800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:53837400-53839800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:53837600-53838800	Enhancers	Fetal Muscle Leg	muscle
25	chr3:53837600-53841800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:53837800-53839400	Enhancers	Fetal Muscle Trunk	muscle
27	chr3:53837800-53839600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:53837800-53839800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:53838000-53838400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:53838000-53838600	Enhancers	NHDF-Ad	bronchial
31	chr3:53838000-53838800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:53838000-53839200	Enhancers	Right Atrium	heart
33	chr3:53838000-53839600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:53838000-53839600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr3:53838000-53840400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:53838000-53841800	Enhancers	Fetal Thymus	thymus
37	chr3:53838200-53839200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:53838200-53839600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:53838200-53839600	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:53838200-53839800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:53838200-53840200	Enhancers	HSMM	muscle
42	chr3:53838200-53841200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:53838200-53841200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:53838200-53841200	Enhancers	NH-A	brain
45	chr3:53838200-53841400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:53838200-53841600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr3:53838200-53841600	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links