Variant report

Variant	rs643980
Chromosome Location	chr16:11973374-11973375
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	chr16:11973175..11975559-chr16:11979030..11980935,2	MCF-7	breast:
2	chr16:11944290..11948249-chr16:11970756..11973644,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263307	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000171490	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11863305	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17235441	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35080834	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs380494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382158	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs407719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs423178	0.81[EUR][1000 genomes]
rs424905	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs435108	0.93[ASN][1000 genomes]
rs449313	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs456485	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs458548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs463767	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs464017	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs464298	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs468517	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs468800	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7184191	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv984257	chr16:11968206-11992901	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11946200-11975600	Weak transcription	Aorta	Aorta
2	chr16:11946400-11975600	Weak transcription	Esophagus	oesophagus
3	chr16:11961400-11975600	Weak transcription	Pancreas	Pancrea
4	chr16:11961600-11986000	Weak transcription	Stomach Mucosa	stomach
5	chr16:11961800-11991000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:11962000-11992200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr16:11962000-11994600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr16:11962200-11992000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr16:11962400-11982600	Strong transcription	Fetal Thymus	thymus
10	chr16:11962400-11984000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr16:11962400-11990800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:11962400-11992000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr16:11962400-11992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr16:11962400-11992200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr16:11962400-11992400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr16:11962400-11995000	Strong transcription	Dnd41	blood
17	chr16:11962600-11985600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr16:11962600-11990600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:11962600-11991800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:11963400-11975000	Weak transcription	Fetal Kidney	kidney
22	chr16:11963800-11974000	Weak transcription	Fetal Brain Male	brain
23	chr16:11963800-11976000	Weak transcription	HSMMtube	muscle
24	chr16:11964800-11990800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr16:11964800-11991000	Strong transcription	Fetal Intestine Large	intestine
26	chr16:11965000-11974200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr16:11965000-11986400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr16:11965000-11990200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:11965000-11991000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr16:11965200-11991000	Strong transcription	GM12878-XiMat	blood
31	chr16:11965400-11990800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr16:11965400-11991400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr16:11965600-11983000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr16:11965600-11983200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr16:11965600-11991000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr16:11965800-11990200	Strong transcription	Liver	Liver
37	chr16:11965800-11995000	Strong transcription	HepG2	liver
38	chr16:11966000-11974000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr16:11966000-11982200	Strong transcription	HUVEC	blood vessel
40	chr16:11966000-11991000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr16:11966000-11991400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr16:11966200-11984200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr16:11966200-11989400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr16:11966200-12006200	Weak transcription	Fetal Heart	heart
45	chr16:11966600-11979800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr16:11966600-11983800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr16:11966600-11988200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr16:11966600-11991000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr16:11967000-11990200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr16:11967400-11974000	Weak transcription	Brain Germinal Matrix	brain

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