Variant report

Variant	rs3826176
Chromosome Location	chr16:48589062-48589063
allele	A/G
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	POLR2A	chr16:48588868-48589100	GM12878	blood:	n/a	n/a
2	ZNF263	chr16:48589009-48589488	HEK293-T-REx	kidney:	n/a	chr16:48589090-48589099

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

Variant related genes	Relation type
N4BP1	TF binding region
ENSG00000261267	TF binding region
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]
rs3785138	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];0.82[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
rs3826176	NOD2	cis	cerebellum	SCAN
rs3826176	C16orf78	cis	cerebellum	SCAN
rs3826176	LCE1B	trans	parietal	SCAN
rs3826176	N4BP1	cis	multi-tissue	Pritchard
rs3826176	PAPD5	cis	cerebellum	SCAN
rs3826176	NKD1	cis	cerebellum	SCAN

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	chr16:48573800-48589400	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr16:48573800-48589800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:48574200-48589400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr16:48574600-48589800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:48576200-48593600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:48577200-48596800	Weak transcription	Colonic Mucosa	Colon
8	chr16:48578200-48592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:48578400-48590600	Weak transcription	Aorta	Aorta
10	chr16:48578400-48593600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:48578400-48601800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:48580800-48594600	Weak transcription	Fetal Kidney	kidney
13	chr16:48581800-48589400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr16:48582200-48589400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr16:48582200-48589400	Weak transcription	Stomach Mucosa	stomach
16	chr16:48582400-48589200	Strong transcription	HepG2	liver
17	chr16:48583200-48589400	Strong transcription	NHEK	skin
18	chr16:48583400-48589400	Strong transcription	Dnd41	blood
19	chr16:48583800-48590400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr16:48583800-48617800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr16:48584000-48590000	Weak transcription	Primary B cells from cord blood	blood
22	chr16:48584600-48591200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:48584800-48589600	Weak transcription	NHLF	lung
24	chr16:48585000-48589200	Strong transcription	GM12878-XiMat	blood
25	chr16:48585400-48590200	Weak transcription	NHDF-Ad	bronchial
26	chr16:48585400-48594600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr16:48585600-48589200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
28	chr16:48586200-48589200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr16:48586200-48589600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr16:48586200-48597400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr16:48586400-48589600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:48586400-48593800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr16:48586400-48594400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:48586800-48589800	Weak transcription	HSMMtube	muscle
35	chr16:48587000-48589800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr16:48587000-48590200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr16:48587000-48590600	Weak transcription	K562	blood
38	chr16:48587000-48592200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr16:48587000-48592400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr16:48587200-48590600	Weak transcription	HUVEC	blood vessel
41	chr16:48587200-48592200	Enhancers	Brain Cingulate Gyrus	brain
42	chr16:48587400-48589800	Weak transcription	HMEC	breast
43	chr16:48587400-48591200	Enhancers	Brain Substantia Nigra	brain
44	chr16:48587400-48594400	Weak transcription	Fetal Thymus	thymus
45	chr16:48587400-48594800	Enhancers	Fetal Heart	heart
46	chr16:48587600-48589600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr16:48587600-48589800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr16:48587600-48590000	Weak transcription	A549	lung
49	chr16:48587600-48591000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr16:48587800-48589200	Genic enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links