Variant report

Variant	rs12918327
Chromosome Location	chr16:30626616-30626617
allele	C/T
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	ELF1	chr16:30626573-30627060	GM12878	blood:	n/a	n/a
2	CTCF	chr16:30626593-30627087	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr16:30626536-30627280	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr16:30626281-30627298	A549	lung:	n/a	n/a
5	YY1	chr16:30626544-30627140	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr16:30626570-30627071	H1-hESC	embryonic stem cell:	n/a	chr16:30626792-30626802 chr16:30626957-30626968
7	RAD21	chr16:30626598-30627064	H1-hESC	embryonic stem cell:	n/a	chr16:30626797-30626811
8	RAD21	chr16:30626534-30627192	HCT-116	colon:	n/a	chr16:30626797-30626811
9	CTCF	chr16:30626540-30626690	HFF-Myc	foreskin:	n/a	n/a
10	EBF1	chr16:30626586-30626976	GM12878	blood:	n/a	n/a
11	TEAD4	chr16:30626589-30627039	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr16:30626552-30627141	A549	lung:	n/a	chr16:30626941-30626951
13	RAD21	chr16:30626604-30627065	HepG2	liver:	n/a	chr16:30626797-30626811
14	RAD21	chr16:30626483-30627106	HepG2	liver:	n/a	chr16:30626797-30626811
15	CBX3	chr16:30626616-30627014	K562	blood:	n/a	n/a
16	CTCF	chr16:30626513-30627184	HCT-116	colon:	n/a	n/a
17	RAD21	chr16:30626571-30627129	A549	lung:	n/a	chr16:30626797-30626811
18	RAD21	chr16:30626489-30627126	A549	lung:	n/a	chr16:30626797-30626811
19	RAD21	chr16:30626514-30627078	H1-hESC	embryonic stem cell:	n/a	chr16:30626797-30626811
20	CTCF	chr16:30626540-30626690	WI-38	lung:	n/a	n/a
21	RAD21	chr16:30626576-30627116	ECC-1	luminal epithelium:	n/a	chr16:30626797-30626811
22	MXI1	chr16:30626417-30627432	SK-N-SH	brain:	n/a	n/a
23	MAX	chr16:30626488-30627142	A549	lung:	n/a	chr16:30626792-30626802 chr16:30626957-30626968
24	RAD21	chr16:30626507-30627123	HCT-116	colon:	n/a	chr16:30626797-30626811
25	EBF1	chr16:30626554-30627045	GM12878	blood:	n/a	n/a
26	RAD21	chr16:30626602-30627069	H1-hESC	embryonic stem cell:	n/a	chr16:30626797-30626811
27	CTCF	chr16:30626565-30627067	HepG2	liver:	n/a	n/a
28	PAX5	chr16:30626607-30626954	GM12878	blood:	n/a	n/a
29	CTCF	chr16:30626585-30627007	MCF-7	breast:	n/a	n/a
30	CTCF	chr16:30626575-30627116	A549	lung:	n/a	n/a
31	RAD21	chr16:30626521-30627303	SK-N-SH	brain:	n/a	chr16:30626797-30626811
32	MAX	chr16:30626593-30627084	H1-hESC	embryonic stem cell:	n/a	chr16:30626792-30626802 chr16:30626957-30626968
33	RAD21	chr16:30626532-30627131	MCF-7	breast:	n/a	chr16:30626797-30626811
34	TCF12	chr16:30626568-30627039	HepG2	liver:	n/a	chr16:30626941-30626951
35	RAD21	chr16:30626569-30627088	MCF-7	breast:	n/a	chr16:30626797-30626811
36	YY1	chr16:30626606-30626971	GM12878	blood:	n/a	n/a
37	CTCF	chr16:30626615-30627010	K562	blood:	n/a	n/a
38	MYC	chr16:30626497-30627049	A549	lung:	n/a	chr16:30626792-30626802 chr16:30626957-30626968
39	RUNX3	chr16:30626604-30626961	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30625309..30627910-chr16:30669048..30671707,2	K562	blood:
2	chr16:30456792..30458556-chr16:30625138..30628133,2	MCF-7	breast:
3	chr16:30620868..30623265-chr16:30625688..30628872,3	K562	blood:
4	chr16:30441433..30442036-chr16:30626398..30626928,2	K562	blood:
5	chr16:30626410..30628513-chr16:30668495..30670548,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF785-4	chr16:30626577-30627000	NONHSAT141782

Variant related genes	Relation type
ZNF689	TF binding region
ENSG00000156853	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000179918	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs13338946	0.94[CHD][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs2289442	0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs28728333	0.98[ASN][1000 genomes]
rs28841118	0.98[ASN][1000 genomes]
rs34114657	0.89[EUR][1000 genomes]
rs34699226	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35629860	0.94[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap]
rs35661204	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36063822	0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap]
rs36064568	0.92[ASN][1000 genomes]
rs3747481	0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs3747486	0.94[CHD][hapmap]
rs3812999	0.94[CHD][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs4485386	0.98[ASN][1000 genomes]
rs4889490	0.94[CHD][hapmap]
rs55875685	0.91[ASN][1000 genomes]
rs6565195	0.96[ASN][1000 genomes]
rs67693285	0.98[ASN][1000 genomes]
rs7184055	0.87[ASN][1000 genomes]
rs7185620	0.98[ASN][1000 genomes]
rs7186852	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7187071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7187359	0.94[CHD][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs7187802	0.87[ASN][1000 genomes]
rs7188789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7191389	0.98[ASN][1000 genomes]
rs7191761	0.98[ASN][1000 genomes]
rs7194347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7197475	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7198250	0.94[CHD][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs7204632	0.98[ASN][1000 genomes]
rs7499339	0.96[ASN][1000 genomes]
rs8058578	0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs8058961	0.94[CHD][hapmap];0.86[MEX][hapmap]
rs885107	0.94[CHD][hapmap]
rs9925025	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9927137	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905727	chr16:30564526-30689696	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12918327	PHKG2	cis	parietal	SCAN
rs12918327	ITGAX	cis	parietal	SCAN
rs12918327	ARMC5	cis	parietal	SCAN
rs12918327	C16orf93	cis	parietal	SCAN
rs12918327	MYST1	cis	parietal	SCAN
rs12918327	RNF40	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30622000-30629200	Weak transcription	Lung	lung
2	chr16:30622200-30626800	Weak transcription	Fetal Brain Female	brain
3	chr16:30622200-30626800	Weak transcription	Fetal Intestine Small	intestine
4	chr16:30622200-30629600	Weak transcription	Brain Angular Gyrus	brain
5	chr16:30622200-30630400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr16:30622200-30630400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr16:30622200-30630400	Weak transcription	Fetal Intestine Large	intestine
8	chr16:30622200-30630600	Weak transcription	HSMMtube	muscle
9	chr16:30622400-30631200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr16:30622600-30630400	Weak transcription	Brain Substantia Nigra	brain
11	chr16:30623400-30629000	Weak transcription	Dnd41	blood
12	chr16:30624800-30626800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr16:30625200-30626800	Enhancers	Primary B cells from peripheral blood	blood
14	chr16:30625200-30626800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:30625200-30626800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr16:30625200-30627400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:30625800-30626800	Enhancers	HepG2	liver
18	chr16:30625800-30629000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr16:30625800-30629200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr16:30626400-30628400	Enhancers	Brain Germinal Matrix	brain
21	chr16:30626600-30626800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr16:30626600-30626800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr16:30626600-30626800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr16:30626600-30626800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr16:30626600-30626800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr16:30626600-30626800	Enhancers	Fetal Thymus	thymus
27	chr16:30626600-30626800	Enhancers	Pancreas	Pancrea
28	chr16:30626600-30626800	Enhancers	GM12878-XiMat	blood
29	chr16:30626600-30627000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr16:30626600-30627000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr16:30626600-30627000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr16:30626600-30627000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr16:30626600-30627000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr16:30626600-30627000	Bivalent Enhancer	Colonic Mucosa	Colon
35	chr16:30626600-30627000	Enhancers	Fetal Muscle Leg	muscle
36	chr16:30626600-30627000	Enhancers	Gastric	stomach
37	chr16:30626600-30627200	Enhancers	Fetal Brain Male	brain
38	chr16:30626600-30627200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr16:30626600-30627400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:30626600-30627400	Enhancers	Duodenum Mucosa	Duodenum
41	chr16:30626600-30627400	Enhancers	Fetal Kidney	kidney
42	chr16:30626600-30627400	Enhancers	Fetal Lung	lung
43	chr16:30626600-30627400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr16:30626600-30627600	Enhancers	A549	lung
45	chr16:30626600-30627600	Enhancers	K562	blood

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