Variant report

Variant	rs935939
Chromosome Location	chr16:81050965-81050966
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr16:81050838-81051228	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81049357..81051775-chr16:81129457..81132672,3	K562	blood:
2	chr16:81049357..81051527-chr16:81129457..81131471,2	K562	blood:
3	chr16:81037094..81043910-chr16:81050858..81058489,11	MCF-7	breast:

Variant related genes	Relation type
CENPN	TF binding region
ENSG00000140905	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000166451	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12917718	1.00[AMR][1000 genomes]
rs1463286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16944340	1.00[YRI][hapmap]
rs16944343	1.00[YRI][hapmap]
rs2084960	1.00[AMR][1000 genomes]
rs2084961	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2084962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2317088	1.00[AMR][1000 genomes]
rs2549851	0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2602422	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2602445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2911153	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2911154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35109118	1.00[AMR][1000 genomes]
rs4888119	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889238	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55735411	1.00[AMR][1000 genomes]
rs6564817	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6564823	1.00[AMR][1000 genomes]
rs7193361	1.00[AMR][1000 genomes]
rs74028849	1.00[AMR][1000 genomes]
rs804884	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs804891	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8050760	1.00[AMR][1000 genomes]
rs935940	1.00[YRI][hapmap];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	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv995083	chr16:81050917-81076406	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81041800-81053600	Weak transcription	Gastric	stomach
2	chr16:81041800-81069000	Weak transcription	Ovary	ovary
3	chr16:81041800-81069000	Weak transcription	Small Intestine	intestine
4	chr16:81042000-81053000	Weak transcription	Brain Angular Gyrus	brain
5	chr16:81042000-81053600	Weak transcription	HSMMtube	muscle
6	chr16:81042000-81054400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr16:81042000-81054800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr16:81042000-81057600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr16:81042000-81058400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr16:81042000-81069000	Weak transcription	Esophagus	oesophagus
11	chr16:81042000-81069000	Weak transcription	Pancreas	Pancrea
12	chr16:81042000-81069600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr16:81042200-81052200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr16:81042200-81053600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr16:81042200-81058600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr16:81042200-81068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr16:81042200-81069000	Weak transcription	Colonic Mucosa	Colon
18	chr16:81042200-81069600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr16:81042400-81052400	Weak transcription	Brain Hippocampus Middle	brain
20	chr16:81042400-81056200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr16:81042400-81069000	Weak transcription	Brain Germinal Matrix	brain
22	chr16:81042400-81069000	Weak transcription	Fetal Heart	heart
23	chr16:81042600-81064200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr16:81043000-81059200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr16:81043000-81063800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr16:81043000-81064600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr16:81043000-81065400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr16:81043200-81062800	Strong transcription	K562	blood
29	chr16:81043200-81065200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr16:81043400-81058800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr16:81044000-81055600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr16:81044000-81057400	Strong transcription	HepG2	liver
33	chr16:81044000-81064400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr16:81044000-81065200	Strong transcription	Thymus	Thymus
35	chr16:81044400-81055800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr16:81044400-81058800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr16:81044400-81059200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr16:81044400-81064000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr16:81044600-81058400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr16:81044600-81064000	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr16:81044800-81053600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr16:81044800-81058800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr16:81044800-81059000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr16:81044800-81065200	Strong transcription	Hela-S3	cervix
45	chr16:81045000-81051600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:81045000-81058200	Strong transcription	HUVEC	blood vessel
47	chr16:81045000-81058800	Strong transcription	Fetal Thymus	thymus
48	chr16:81045000-81064000	Strong transcription	Dnd41	blood
49	chr16:81045200-81062800	Strong transcription	Osteobl	bone
50	chr16:81045200-81065200	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links