Variant report

Variant	rs16854493
Chromosome Location	chr3:143567923-143567924
allele	A/G
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	NFIC	chr3:143566543-143567950	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143566553..143569042-chr3:143690803..143692633,2	MCF-7	breast:

Variant related genes	Relation type
SLC9A9	TF binding region
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10433437	0.90[CHB][hapmap]
rs10513230	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10513231	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10513232	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11920369	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12497227	0.90[CHB][hapmap]
rs1394403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1504605	0.85[JPT][hapmap]
rs16854417	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16854421	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16854423	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16854424	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.82[YRI][hapmap]
rs16854463	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs16854503	0.90[CHB][hapmap]
rs16854525	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17275413	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1823220	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1900643	0.90[CHB][hapmap]
rs1989180	0.90[CHB][hapmap]
rs2361199	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2361204	0.90[CHB][hapmap]
rs4839613	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4839614	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4839659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4839660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4839661	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4839663	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4839670	0.90[CHB][hapmap]
rs55734708	0.82[ASN][1000 genomes]
rs55904283	0.81[AMR][1000 genomes]
rs56010653	0.90[AMR][1000 genomes]
rs56117352	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs60765943	0.84[ASN][1000 genomes]
rs61574504	0.86[ASN][1000 genomes]
rs6440202	0.85[JPT][hapmap]
rs6764661	0.90[CHB][hapmap]
rs6765414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6769847	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6776336	0.90[CHB][hapmap]
rs6792031	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6799226	0.82[JPT][hapmap]
rs6804065	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72997334	0.90[AMR][1000 genomes]
rs73008747	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73871853	0.82[ASN][1000 genomes]
rs73871854	0.82[ASN][1000 genomes]
rs73871855	0.82[ASN][1000 genomes]
rs7621206	0.90[CHB][hapmap]
rs7651412	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7652644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs924851	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs951594	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs951595	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9822158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9827103	0.90[CHB][hapmap]
rs9832471	0.90[CHB][hapmap]
rs9847107	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143565800-143569200	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:143566000-143568200	Active TSS	Brain Anterior Caudate	brain
3	chr3:143566000-143568400	Active TSS	Ovary	ovary
4	chr3:143566200-143568000	Active TSS	Brain Cingulate Gyrus	brain
5	chr3:143566200-143568600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr3:143567400-143568000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:143567400-143568000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr3:143567400-143568000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:143567400-143568000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:143567400-143568200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:143567400-143568200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr3:143567400-143568400	Enhancers	Fetal Thymus	thymus
13	chr3:143567400-143568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:143567400-143569000	Enhancers	HSMM	muscle
15	chr3:143567400-143569000	Enhancers	NHEK	skin
16	chr3:143567400-143570000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr3:143567400-143570600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:143567400-143571000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:143567600-143568000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:143567600-143568000	Enhancers	Psoas Muscle	Psoas
21	chr3:143567600-143568000	Flanking Active TSS	GM12878-XiMat	blood
22	chr3:143567600-143568200	Enhancers	Primary B cells from cord blood	blood
23	chr3:143567600-143568400	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr3:143567600-143568400	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr3:143567600-143569000	Enhancers	HMEC	breast
26	chr3:143567600-143569200	Enhancers	Fetal Stomach	stomach
27	chr3:143567600-143569200	Enhancers	HUVEC	blood vessel
28	chr3:143567600-143569400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:143567600-143569600	Enhancers	Primary T cells from cord blood	blood
30	chr3:143567600-143569600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:143567600-143569600	Enhancers	HSMMtube	muscle
32	chr3:143567800-143568000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:143567800-143568000	Enhancers	Brain Angular Gyrus	brain
34	chr3:143567800-143568000	Enhancers	Rectal Smooth Muscle	rectum
35	chr3:143567800-143568000	Active TSS	NHDF-Ad	bronchial
36	chr3:143567800-143568200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:143567800-143568200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr3:143567800-143568200	Enhancers	Dnd41	blood
39	chr3:143567800-143568400	Enhancers	Adipose Nuclei	Adipose
40	chr3:143567800-143568600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:143567800-143568600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:143567800-143568600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:143567800-143568600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:143567800-143568600	Weak transcription	Fetal Lung	lung
45	chr3:143567800-143568600	Weak transcription	Osteobl	bone
46	chr3:143567800-143568800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:143567800-143568800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:143567800-143568800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:143567800-143568800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:143567800-143569000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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