Variant report

Variant	rs3812079
Chromosome Location	chr5:177550476-177550477
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177548762..177553216-chr5:177630602..177633012,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197451	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10035478	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10042021	0.82[EUR][1000 genomes]
rs10060446	0.80[ASN][1000 genomes]
rs13163671	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13180226	0.89[CEU][hapmap];0.90[CHB][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13185017	0.88[ASN][1000 genomes]
rs13189047	0.90[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs13436876	0.81[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34093388	0.80[ASN][1000 genomes]
rs35027513	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35885458	0.82[ASN][1000 genomes]
rs36087128	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36090803	0.84[ASN][1000 genomes]
rs3812073	0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs3812074	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812075	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812077	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812080	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3924305	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4637566	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601217	0.85[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap]
rs6601220	0.80[AMR][1000 genomes]
rs6873523	0.81[ASW][hapmap];0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6893797	0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7379278	0.86[CHB][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7380934	0.94[GIH][hapmap];0.82[MEX][hapmap]
rs7380947	0.82[EUR][1000 genomes]
rs7447860	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7701678	0.88[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7716409	0.83[ASN][1000 genomes]
rs7732415	0.82[CHB][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
3	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
5	nsv462567	chr5:177505021-177572927	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv471058	chr5:177505021-177572927	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv600392	chr5:177505021-177572927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
9	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv883191	chr5:177535370-177551985	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv883192	chr5:177535370-177564346	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv600394	chr5:177549491-177608195	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3812079	DCTN3	trans	parietal	SCAN
rs3812079	DOK3	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177541800-177557200	Weak transcription	Right Atrium	heart
2	chr5:177542600-177551000	Weak transcription	Gastric	stomach
3	chr5:177544600-177552200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:177545200-177552000	Enhancers	Fetal Thymus	thymus
5	chr5:177546200-177551400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:177546200-177551800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:177546200-177552000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:177546400-177552200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:177546600-177551000	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr5:177546600-177551000	Genic enhancers	Placenta	Placenta
11	chr5:177547000-177553400	Weak transcription	HUVEC	blood vessel
12	chr5:177547800-177550600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:177548000-177550800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:177548000-177550800	Weak transcription	Fetal Brain Female	brain
15	chr5:177548000-177550800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr5:177548200-177550600	Enhancers	Left Ventricle	heart
17	chr5:177548200-177551600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:177548400-177551600	Enhancers	Right Ventricle	heart
19	chr5:177548600-177550600	Weak transcription	Stomach Mucosa	stomach
20	chr5:177548600-177550800	Weak transcription	K562	blood
21	chr5:177548600-177551400	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr5:177548600-177551400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr5:177548600-177551400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr5:177548600-177557000	Weak transcription	Fetal Intestine Large	intestine
25	chr5:177548800-177550600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:177548800-177550800	Weak transcription	HSMMtube	muscle
27	chr5:177548800-177551200	Weak transcription	Brain Germinal Matrix	brain
28	chr5:177548800-177551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:177548800-177557000	Weak transcription	Fetal Intestine Small	intestine
30	chr5:177548800-177557200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr5:177549000-177552200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:177549200-177550600	Enhancers	Psoas Muscle	Psoas
33	chr5:177549200-177550800	Weak transcription	NHEK	skin
34	chr5:177549200-177552800	Genic enhancers	Fetal Stomach	stomach
35	chr5:177549200-177553600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:177549400-177551200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr5:177549400-177551600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:177549400-177552800	Genic enhancers	Fetal Muscle Leg	muscle
39	chr5:177549400-177553000	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr5:177549400-177554800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:177549400-177557200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:177549400-177558200	Weak transcription	Fetal Heart	heart
43	chr5:177549600-177550600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:177549600-177550600	Weak transcription	Spleen	Spleen
45	chr5:177549600-177551000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr5:177549600-177551400	Genic enhancers	H1 Cell Line	embryonic stem cell
47	chr5:177549600-177551800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr5:177549600-177557000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:177549600-177557200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:177549600-177557400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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