Variant report

Variant	rs4955793
Chromosome Location	chr3:178782021-178782022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178780357..178782332-chr3:178782506..178785505,2	MCF-7	breast:
2	chr3:178780519..178783087-chr3:178791350..178793561,2	MCF-7	breast:
3	chr3:178781078..178783902-chr3:178788373..178789943,2	MCF-7	breast:
4	chr3:178781504..178783011-chr3:178869309..178871100,2	K562	blood:

Variant related genes	Relation type
ENSG00000172667	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13320527	1.00[GIH][hapmap];0.82[TSI][hapmap]
rs4395443	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4854955	1.00[GIH][hapmap];0.82[TSI][hapmap]
rs4855094	1.00[GIH][hapmap];0.82[TSI][hapmap]
rs61796654	0.86[AMR][1000 genomes]
rs61798160	0.86[AMR][1000 genomes]
rs61798202	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804195	1.00[GIH][hapmap];0.82[TSI][hapmap]
rs7642068	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9872959	1.00[GIH][hapmap];0.82[TSI][hapmap]

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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
5	nsv1009143	chr3:178731525-178783915	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	esv1799481	chr3:178733212-178782021	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Post-traumatic stress disorder (asjusted for relatedness)	23726511	GWAS catalog

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178746000-178784000	Weak transcription	Liver	Liver
2	chr3:178746000-178785200	Weak transcription	Thymus	Thymus
3	chr3:178753600-178784800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:178755600-178787800	Weak transcription	Aorta	Aorta
5	chr3:178756000-178783600	Weak transcription	NHDF-Ad	bronchial
6	chr3:178756600-178783800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:178756800-178788400	Weak transcription	Fetal Intestine Small	intestine
8	chr3:178756800-178788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:178757200-178782200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:178764200-178787000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:178764400-178784600	Weak transcription	K562	blood
12	chr3:178764600-178782400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:178764800-178785200	Weak transcription	Pancreas	Pancrea
14	chr3:178764800-178787200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:178764800-178789000	Weak transcription	Lung	lung
16	chr3:178765000-178785400	Weak transcription	Gastric	stomach
17	chr3:178765000-178786800	Weak transcription	Dnd41	blood
18	chr3:178765200-178784600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:178765200-178789000	Weak transcription	Spleen	Spleen
20	chr3:178768400-178784000	Weak transcription	HUVEC	blood vessel
21	chr3:178768400-178788800	Weak transcription	Small Intestine	intestine
22	chr3:178768600-178788800	Weak transcription	Placenta	Placenta
23	chr3:178769200-178784000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:178769600-178782200	Weak transcription	Primary B cells from cord blood	blood
25	chr3:178769800-178783800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:178770000-178783800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:178770200-178784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:178770600-178784800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:178770800-178783800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:178771000-178788400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:178771600-178784800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:178772000-178786800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:178772600-178782600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:178772600-178788800	Weak transcription	Esophagus	oesophagus
35	chr3:178773000-178782200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:178773600-178788600	Weak transcription	Fetal Stomach	stomach
37	chr3:178773800-178784600	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:178774000-178782800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr3:178774000-178784000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:178774400-178784600	Weak transcription	Fetal Intestine Large	intestine
41	chr3:178774600-178782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:178775000-178786000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:178776000-178784000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:178776000-178784000	Weak transcription	Adipose Nuclei	Adipose
45	chr3:178776000-178784800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:178777400-178782200	Strong transcription	HSMM	muscle
47	chr3:178777800-178782200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:178777800-178788400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:178778000-178783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:178778200-178788600	Weak transcription	Primary hematopoietic stem cells	blood

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