Variant report

Variant	rs352646
Chromosome Location	chr3:52205800-52205801
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52205035..52206671-chr3:52208297..52209817,2	K562	blood:
2	chr3:52188433..52190698-chr3:52204097..52207036,3	MCF-7	breast:
3	chr3:52205020..52207275-chr3:52207842..52209830,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164087	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs323888	1.00[AMR][1000 genomes]
rs323899	1.00[AMR][1000 genomes]
rs323901	1.00[AMR][1000 genomes]
rs35898691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57236484	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59196507	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61333587	1.00[AMR][1000 genomes]
rs6446153	1.00[AMR][1000 genomes]
rs72955239	1.00[AMR][1000 genomes]
rs72955243	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955259	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955260	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964041	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52196200-52210400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:52204800-52206200	Enhancers	Fetal Intestine Small	intestine
3	chr3:52204800-52206200	Enhancers	K562	blood
4	chr3:52204800-52206400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:52204800-52215600	Weak transcription	Right Ventricle	heart
6	chr3:52205000-52206400	Enhancers	Duodenum Mucosa	Duodenum
7	chr3:52205000-52206400	Enhancers	NHDF-Ad	bronchial
8	chr3:52205000-52206400	Enhancers	NHLF	lung
9	chr3:52205000-52206600	Enhancers	Hela-S3	cervix
10	chr3:52205200-52206200	Enhancers	A549	lung
11	chr3:52205200-52206600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:52205400-52205800	Enhancers	Fetal Intestine Large	intestine
13	chr3:52205400-52206000	Enhancers	HSMM	muscle
14	chr3:52205400-52206000	Enhancers	HSMMtube	muscle
15	chr3:52205400-52206000	Enhancers	Osteobl	bone
16	chr3:52205400-52206200	Enhancers	HepG2	liver
17	chr3:52205400-52207400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:52205400-52207600	Enhancers	Brain Hippocampus Middle	brain
19	chr3:52205400-52207600	Enhancers	Brain Substantia Nigra	brain
20	chr3:52205400-52208800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:52205400-52209200	Weak transcription	Spleen	Spleen
22	chr3:52205400-52210200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:52205600-52206000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:52205600-52206000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:52205600-52206200	Enhancers	Stomach Mucosa	stomach
26	chr3:52205600-52207400	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:52205800-52206000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:52205800-52206000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:52205800-52206200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:52205800-52206200	Enhancers	Gastric	stomach
31	chr3:52205800-52206200	Enhancers	NHEK	skin
32	chr3:52205800-52206600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links