Variant report

Variant	rs16854935
Chromosome Location	chr1:179872502-179872503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr1:179872430-179872550	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:179872398-179872684	SK-N-MC	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179850058..179853356-chr1:179869131..179876291,8	K562	blood:
2	chr1:179849896..179853295-chr1:179868800..179873439,8	K562	blood:
3	chr1:179851750..179853316-chr1:179871986..179873575,2	MCF-7	breast:
4	chr1:179850426..179852030-chr1:179871802..179874421,2	MCF-7	breast:
5	chr1:179866194..179868046-chr1:179871129..179873011,2	K562	blood:

No data

Variant related genes	Relation type
TOR1AIP1	TF binding region
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10436866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12239940	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13374504	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854828	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854841	1.00[AMR][1000 genomes]
rs16854843	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854853	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854861	0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854895	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854908	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854952	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs56725488	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59284984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59961638	0.89[AFR][1000 genomes];1.00[AMR][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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription 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	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
2	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
7	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
9	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
10	chr1:179856200-179876800	Weak transcription	NHLF	lung
11	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
12	chr1:179860000-179873800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:179860200-179890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:179860400-179873000	Weak transcription	HUVEC	blood vessel
15	chr1:179860400-179873200	Weak transcription	K562	blood
16	chr1:179860400-179878800	Weak transcription	Colonic Mucosa	Colon
17	chr1:179861200-179878000	Weak transcription	Gastric	stomach
18	chr1:179861200-179886600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:179861400-179882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:179861600-179872600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:179861600-179872600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:179861600-179886600	Weak transcription	Pancreas	Pancrea
23	chr1:179863000-179876800	Weak transcription	Fetal Kidney	kidney
24	chr1:179863200-179877400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:179867200-179886600	Weak transcription	Small Intestine	intestine
26	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
27	chr1:179868000-179873800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:179868200-179879800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr1:179868200-179880800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:179868200-179891600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:179868200-179891800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:179868400-179877600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr1:179868400-179880600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:179868400-179880600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:179868400-179888800	Strong transcription	Adipose Nuclei	Adipose
36	chr1:179868400-179890600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:179868400-179890800	Strong transcription	Dnd41	blood
38	chr1:179868600-179872800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:179868600-179891600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:179868600-179892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:179868800-179876400	Strong transcription	Fetal Lung	lung
42	chr1:179868800-179889000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:179868800-179889200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:179868800-179889600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:179869000-179875600	Strong transcription	Fetal Intestine Large	intestine
46	chr1:179869000-179879000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:179869000-179888200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:179869200-179875000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:179869200-179875800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:179869200-179879600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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