Variant report

Variant	rs9899944
Chromosome Location	chr17:16488590-16488591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16487641..16489428-chr17:16491263..16493497,2	MCF-7	breast:
2	chr17:16438778..16440938-chr17:16486028..16489124,4	MCF-7	breast:
3	chr17:16471107..16473836-chr17:16487163..16489402,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141040	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11868291	0.95[EUR][1000 genomes]
rs11870650	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870734	1.00[ASN][1000 genomes]
rs16959837	1.00[ASN][1000 genomes]
rs2058197	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28419755	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28704561	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57240543	1.00[ASN][1000 genomes]
rs59771043	0.96[EUR][1000 genomes]
rs60644317	1.00[ASN][1000 genomes]
rs62072767	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62072768	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62072769	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072771	0.96[EUR][1000 genomes]
rs62072772	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072773	0.87[ASN][1000 genomes]
rs62072776	0.95[EUR][1000 genomes]
rs62072777	0.95[EUR][1000 genomes]
rs62072778	0.95[EUR][1000 genomes]
rs62072782	0.83[EUR][1000 genomes]
rs62072783	0.83[EUR][1000 genomes]
rs62072785	0.83[EUR][1000 genomes]
rs62072786	0.83[EUR][1000 genomes]
rs62072787	0.83[EUR][1000 genomes]
rs62072789	0.83[EUR][1000 genomes]
rs62072791	0.83[EUR][1000 genomes]
rs62072846	0.83[EUR][1000 genomes]
rs62072847	0.83[EUR][1000 genomes]
rs62072856	0.83[EUR][1000 genomes]
rs62072857	0.83[EUR][1000 genomes]
rs62072858	0.83[EUR][1000 genomes]
rs62072859	0.83[EUR][1000 genomes]
rs62073662	0.83[EUR][1000 genomes]
rs62073663	0.83[EUR][1000 genomes]
rs62073665	0.83[EUR][1000 genomes]
rs62073667	0.83[EUR][1000 genomes]
rs62073702	0.83[EUR][1000 genomes]
rs62073703	0.83[EUR][1000 genomes]
rs62073705	0.83[EUR][1000 genomes]
rs62073706	0.83[EUR][1000 genomes]
rs62073707	0.83[EUR][1000 genomes]
rs62073708	0.83[EUR][1000 genomes]
rs62073709	0.81[EUR][1000 genomes]
rs62073710	0.83[EUR][1000 genomes]
rs7218473	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224237	0.83[EUR][1000 genomes]
rs73982008	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8065062	0.96[EUR][1000 genomes]
rs8065749	0.91[EUR][1000 genomes]
rs9902115	0.95[EUR][1000 genomes]
rs9909271	0.95[EUR][1000 genomes]
rs9909921	0.95[EUR][1000 genomes]
rs9910496	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS 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	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16488200-16489000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:16488200-16489000	Weak transcription	Fetal Lung	lung
3	chr17:16488200-16489600	Enhancers	Adipose Nuclei	Adipose
4	chr17:16488200-16491800	Weak transcription	Pancreas	Pancrea
5	chr17:16488200-16492000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr17:16488200-16492000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:16488200-16492000	Weak transcription	Liver	Liver
8	chr17:16488200-16492000	Weak transcription	Brain Anterior Caudate	brain
9	chr17:16488200-16492000	Weak transcription	Brain Hippocampus Middle	brain
10	chr17:16488200-16492000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:16488200-16492000	Weak transcription	Brain Substantia Nigra	brain
12	chr17:16488200-16492000	Weak transcription	Colon Smooth Muscle	Colon
13	chr17:16488200-16492000	Weak transcription	Psoas Muscle	Psoas
14	chr17:16488200-16492000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr17:16488200-16492000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr17:16488200-16492200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:16488200-16492200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:16488200-16492200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:16488200-16492200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:16488200-16492200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:16488200-16492200	Weak transcription	Placenta	Placenta
22	chr17:16488200-16492200	Weak transcription	Left Ventricle	heart
23	chr17:16488200-16492200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr17:16488200-16492200	Weak transcription	Right Ventricle	heart
25	chr17:16488200-16492200	Weak transcription	HMEC	breast
26	chr17:16488400-16488600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:16488400-16488800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:16488400-16488800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr17:16488400-16489400	Weak transcription	GM12878-XiMat	blood
30	chr17:16488400-16492000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:16488400-16492000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links