Variant report

Variant	rs13322200
Chromosome Location	chr3:19932419-19932420
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19930617..19933383-chr3:19987388..19990668,4	MCF-7	breast:
2	chr3:19930446..19931966-chr3:19932163..19933731,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13319835	0.85[AFR][1000 genomes]
rs13319903	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28525232	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28750438	0.85[AFR][1000 genomes]
rs9821714	0.80[AFR][1000 genomes]
rs9822567	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9822900	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9826936	0.80[AFR][1000 genomes]
rs9829864	0.97[AFR][1000 genomes]
rs9835667	0.85[AFR][1000 genomes]
rs9840728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9845694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9847723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9848474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9848611	0.82[AFR][1000 genomes]
rs9865514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9873155	1.00[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	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1003183	chr3:19671647-19948351	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19927400-19941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:19930000-19932800	Enhancers	Fetal Stomach	stomach
3	chr3:19930600-19933200	Weak transcription	Gastric	stomach
4	chr3:19931200-19933000	Weak transcription	HMEC	breast
5	chr3:19931400-19932600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:19931400-19932800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:19931400-19933200	Weak transcription	NH-A	brain
8	chr3:19931400-19933400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:19931400-19933800	Enhancers	NHDF-Ad	bronchial
10	chr3:19931400-19934000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:19931600-19932600	Weak transcription	Colonic Mucosa	Colon
12	chr3:19931600-19933000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:19931600-19933000	Weak transcription	NHEK	skin
14	chr3:19931600-19933200	Weak transcription	HSMM	muscle
15	chr3:19931600-19933800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:19931800-19932800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:19931800-19933000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:19931800-19933200	Weak transcription	NHLF	lung
19	chr3:19931800-19940000	Weak transcription	Osteobl	bone
20	chr3:19931800-19940200	Weak transcription	HUVEC	blood vessel
21	chr3:19931800-19943400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:19932000-19933000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:19932000-19933200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:19932400-19932800	Weak transcription	A549	lung
25	chr3:19932400-19933200	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links