Variant report

Variant	rs3785138
Chromosome Location	chr16:48588614-48588615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:48588595-48588912	K562	blood:	n/a	n/a
2	POLR2A	chr16:48588383-48588724	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:48588574-48588624	HEEpiC	esophagus:	n/a
2	chr16:48588574-48588624	NH-A	brain:	n/a
3	chr16:48588574-48588624	HAEpiC	amniotic membrane:	n/a
4	chr16:48588574-48588624	PFSK-1	brain:	n/a
5	chr16:48588574-48588624	HCM	heart:	n/a
6	chr16:48588574-48588624	GM12891	blood:	n/a
7	chr16:48588574-48588624	GM06990	blood:	n/a
8	chr16:48588574-48588624	HCF	heart:	n/a
9	chr16:48588574-48588624	AG09319	gingival:	n/a
10	chr16:48588574-48588624	SAEC	small airway:	n/a
11	chr16:48588574-48588624	BJ	skin:	n/a
12	chr16:48588574-48588624	T-47D	breast:	n/a
13	chr16:48588574-48588624	HepG2	liver:	n/a
14	chr16:48588574-48588624	ECC-1	luminal epithelium:	n/a
15	chr16:48588574-48588624	SKMC	muscle:	n/a
16	chr16:48588574-48588624	SK-N-MC	brain:	n/a
17	chr16:48588574-48588624	HRPEpiC	eye:	n/a
18	chr16:48588574-48588624	GM12878	blood:	n/a
19	chr16:48588574-48588624	LNCaP	prostate:	n/a
20	chr16:48588574-48588624	ProgFib	skin:	n/a
21	chr16:48588574-48588624	HRCEpiC	kidney:	n/a
22	chr16:48588574-48588624	NHDF-neo	bronchial:	n/a
23	chr16:48588574-48588624	CMK	blood:	n/a
24	chr16:48588574-48588624	HIPEpiC	eye:	n/a
25	chr16:48588574-48588624	AG04450	lung:	fetal
26	chr16:48588574-48588624	PANC-1	pancreas:	n/a
27	chr16:48588574-48588624	GM12892	blood:	n/a
28	chr16:48588574-48588624	GM19239	blood:	n/a
29	chr16:48588574-48588624	MCF10A-Er-Src	breast:	n/a
30	chr16:48588574-48588624	HRE	kidney:	n/a
31	chr16:48588574-48588624	AoSMC	blood vessel:	n/a
32	chr16:48588574-48588624	U87	brain:	n/a
33	chr16:48588574-48588624	H1-hESC	embryonic stem cell:	embryo
34	chr16:48588574-48588624	IMR90	lung:	fetal
35	chr16:48588574-48588624	AG10803	skin:	n/a
36	chr16:48588574-48588624	HCPEpiC	choroid plexus:	n/a
37	chr16:48588574-48588624	ovcar-3	ovarian:	n/a
38	chr16:48588574-48588624	HMEC	breast:	n/a
39	chr16:48588574-48588624	HCT-116	colon:	n/a
40	chr16:48588574-48588624	SK-N-SH_RA	brain:	n/a
41	chr16:48588574-48588624	K562	blood:	n/a
42	chr16:48588574-48588624	HPAEpiC	pulmonary alveolar:	n/a
43	chr16:48588574-48588624	HUVEC	blood vessel:	n/a
44	chr16:48588574-48588624	PrEC	prostate:	n/a
45	chr16:48588574-48588624	SK-N-SH	brain:	n/a
46	chr16:48588574-48588624	HEK293	kidney:	embryo
47	chr16:48588574-48588624	AG04449	skin:	fetal
48	chr16:48588574-48588624	HL-60	blood:	n/a
49	chr16:48588574-48588624	AG09309	skin:	n/a
50	chr16:48588574-48588624	NHBE	bronchial:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48587953..48590507-chr16:48591392..48593667,3	MCF-7	breast:

No data

Variant related genes	Relation type
N4BP1	TF binding region
ENSG00000261267	TF binding region
ENSG00000261267	CpG island
N4BP1	CpG island
ENSG00000261267	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12918232	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1345439	1.00[JPT][hapmap]
rs1420719	1.00[JPT][hapmap]
rs17754748	0.81[ASN][1000 genomes]
rs2047601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3103015	1.00[JPT][hapmap]
rs3826176	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4028695	1.00[CHB][hapmap]
rs4315324	0.87[AMR][1000 genomes]
rs6500392	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6500393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046716	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8057605	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9930255	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3785138	NKD1	cis	cerebellum	SCAN
rs3785138	NOD2	cis	cerebellum	SCAN
rs3785138	PAPD5	cis	cerebellum	SCAN
rs3785138	C16orf78	cis	cerebellum	SCAN
rs3785138	LCE1B	trans	parietal	SCAN
rs3785138	N4BP1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48572400-48592400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:48573800-48588800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:48573800-48589400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:48573800-48589800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr16:48574200-48589400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:48574600-48588800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:48574600-48589800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr16:48575000-48588800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr16:48575000-48589000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr16:48576200-48588800	Strong transcription	Placenta	Placenta
11	chr16:48576200-48593600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr16:48577200-48596800	Weak transcription	Colonic Mucosa	Colon
13	chr16:48578200-48592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr16:48578400-48590600	Weak transcription	Aorta	Aorta
15	chr16:48578400-48593600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr16:48578400-48601800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:48578800-48588800	Weak transcription	Ovary	ovary
18	chr16:48580800-48594600	Weak transcription	Fetal Kidney	kidney
19	chr16:48581800-48589400	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr16:48582200-48589400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr16:48582200-48589400	Weak transcription	Stomach Mucosa	stomach
22	chr16:48582400-48589200	Strong transcription	HepG2	liver
23	chr16:48583200-48589400	Strong transcription	NHEK	skin
24	chr16:48583400-48588800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr16:48583400-48589400	Strong transcription	Dnd41	blood
26	chr16:48583800-48590400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr16:48583800-48617800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr16:48584000-48588800	Weak transcription	Fetal Brain Male	brain
29	chr16:48584000-48590000	Weak transcription	Primary B cells from cord blood	blood
30	chr16:48584600-48591200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr16:48584800-48589600	Weak transcription	NHLF	lung
32	chr16:48585000-48589200	Strong transcription	GM12878-XiMat	blood
33	chr16:48585400-48589000	Weak transcription	Fetal Brain Female	brain
34	chr16:48585400-48590200	Weak transcription	NHDF-Ad	bronchial
35	chr16:48585400-48594600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr16:48585600-48588800	Weak transcription	Brain Germinal Matrix	brain
37	chr16:48585600-48589000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr16:48585600-48589200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
39	chr16:48586200-48588800	Weak transcription	Liver	Liver
40	chr16:48586200-48589000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr16:48586200-48589200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr16:48586200-48589600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr16:48586200-48597400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr16:48586400-48588800	Weak transcription	Pancreas	Pancrea
45	chr16:48586400-48589000	Weak transcription	Esophagus	oesophagus
46	chr16:48586400-48589600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr16:48586400-48593800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr16:48586400-48594400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr16:48586800-48589000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr16:48586800-48589800	Weak transcription	HSMMtube	muscle

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