Variant report

Variant	rs3812089
Chromosome Location	chr5:177633116-177633117
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:3982997..3985280-chr5:177631558..177634299,2	K562	blood:
2	chr5:177556499..177561085-chr5:177629309..177633856,7	K562	blood:
3	chr5:176792166..176794186-chr5:177632419..177635026,2	K562	blood:
4	chr5:176942187..176944181-chr5:177630972..177633765,3	K562	blood:
5	chr5:177588875..177592834-chr5:177630545..177633533,4	K562	blood:
6	chr5:177632239..177635165-chr5:179247019..179248858,2	K562	blood:
7	chr5:177578534..177581104-chr5:177631476..177634038,2	MCF-7	breast:
8	chr5:177591354..177594975-chr5:177630282..177634044,5	MCF-7	breast:
9	chr5:177572705..177577722-chr5:177630592..177633512,5	MCF-7	breast:
10	chr17:59477135..59479003-chr5:177630296..177633273,2	MCF-7	breast:
11	chr5:177578478..177582579-chr5:177629428..177633237,12	MCF-7	breast:
12	chr5:177631720..177633728-chr6:25726576..25729132,2	K562	blood:
13	chr5:177631876..177633528-chr5:179047045..179049302,2	MCF-7	breast:
14	chr5:177555803..177560183-chr5:177628551..177633825,8	MCF-7	breast:
15	chr5:177568592..177570567-chr5:177631471..177633175,2	MCF-7	breast:
16	chr5:177538337..177541901-chr5:177630904..177633261,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167658	Chromatin interaction
ENSG00000145911	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000146047	Chromatin interaction
ENSG00000183258	Chromatin interaction
ENSG00000251211	Chromatin interaction
ENSG00000145912	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000169220	Chromatin interaction
ENSG00000164508	Chromatin interaction
ENSG00000145916	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1366223	0.82[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.97[ASN][1000 genomes]
rs2913746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2913817	0.85[AMR][1000 genomes]
rs2913863	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2913868	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2961678	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2961683	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62388715	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1017664	chr5:177578194-177633116	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
5	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer 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	106 gene(s)	inside rSNPs	diseases
6	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
7	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
8	esv3404661	chr5:177629746-177634244	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	diseases
9	nsv820182	chr5:177630926-177634191	Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
10	esv3373194	chr5:177630971-177633519	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3812089	DBN1	cis	cerebellum	SCAN
rs3812089	NSD1	cis	parietal	SCAN
rs3812089	UNC5A	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177630800-177633200	Active TSS	Gastric	stomach
2	chr5:177630800-177633200	Active TSS	Lung	lung
3	chr5:177630800-177633400	Active TSS	Esophagus	oesophagus
4	chr5:177630800-177633400	Active TSS	Left Ventricle	heart
5	chr5:177630800-177633800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:177631000-177634000	Active TSS	HSMMtube	muscle
7	chr5:177631200-177633400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:177631400-177633200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:177631800-177633200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:177631800-177633200	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr5:177631800-177633200	Active TSS	Aorta	Aorta
12	chr5:177632400-177633200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr5:177632400-177633200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:177632400-177633200	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr5:177632400-177633400	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr5:177632400-177633400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr5:177632400-177633400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr5:177632400-177633600	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
19	chr5:177632400-177633600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:177632400-177633600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr5:177632400-177633600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr5:177632400-177633800	Flanking Active TSS	Colonic Mucosa	Colon
23	chr5:177632400-177633800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr5:177632400-177633800	Transcr. at gene 5' and 3'	NHEK	skin
25	chr5:177632400-177634000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:177632400-177634000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:177632400-177634200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
28	chr5:177632400-177634200	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:177632400-177634200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:177632400-177634400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:177632400-177634600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
32	chr5:177632400-177635000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
33	chr5:177632400-177635000	Transcr. at gene 5' and 3'	K562	blood
34	chr5:177632400-177635200	Transcr. at gene 5' and 3'	Dnd41	blood
35	chr5:177632600-177633200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr5:177632600-177633200	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr5:177632600-177633200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:177632600-177633200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:177632600-177633200	Flanking Active TSS	Liver	Liver
40	chr5:177632600-177633200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr5:177632600-177633200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:177632600-177633200	Flanking Active TSS	Fetal Brain Female	brain
43	chr5:177632600-177633200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr5:177632600-177633200	Flanking Bivalent TSS/Enh	HepG2	liver
45	chr5:177632600-177633400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr5:177632600-177633400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr5:177632600-177633400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:177632600-177633400	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr5:177632600-177633400	Transcr. at gene 5' and 3'	Placenta	Placenta
50	chr5:177632600-177633400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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