Variant report

Variant	rs8046716
Chromosome Location	chr16:48560941-48560942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:48559845..48562587-chr16:48571698..48574105,2	K562	blood:
2	chr16:48387226..48388138-chr16:48560079..48561124,3	MCF-7	breast:
3	chr16:48267927..48268788-chr16:48560181..48561094,2	MCF-7	breast:
4	chr16:48560129..48561061-chr16:48657041..48657742,3	MCF-7	breast:
5	chr16:48417609..48422377-chr16:48557462..48561956,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196470	Chromatin interaction
ENSG00000260086	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001872	0.91[ASN][1000 genomes]
rs1004704	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11076569	0.85[ASN][1000 genomes]
rs11643514	0.81[ASN][1000 genomes]
rs11648225	0.84[ASN][1000 genomes]
rs12918232	0.89[AMR][1000 genomes]
rs1566466	0.81[ASN][1000 genomes]
rs1566467	0.81[ASN][1000 genomes]
rs1948713	0.94[ASN][1000 genomes]
rs2047601	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2062553	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2062554	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2062555	0.84[ASN][1000 genomes]
rs2088753	0.81[ASN][1000 genomes]
rs2088754	0.81[ASN][1000 genomes]
rs2354580	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3785138	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]
rs3826176	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]
rs4315324	0.85[AMR][1000 genomes]
rs4785244	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4785520	0.81[ASN][1000 genomes]
rs4785521	0.85[ASN][1000 genomes]
rs55745119	0.84[ASN][1000 genomes]
rs6500390	0.88[ASN][1000 genomes]
rs6500392	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6500393	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7184700	0.85[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs7198420	0.85[CHB][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs7202699	0.94[ASN][1000 genomes]
rs7206781	0.85[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs8052026	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs8054389	0.92[ASN][1000 genomes]
rs8056201	0.84[ASN][1000 genomes]
rs8056346	0.84[ASN][1000 genomes]
rs8057027	0.91[ASN][1000 genomes]
rs8057605	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8063059	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs9921402	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs9923092	0.81[ASN][1000 genomes]
rs9925108	0.94[ASN][1000 genomes]
rs9926683	0.81[ASN][1000 genomes]
rs9930255	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9933892	0.84[ASN][1000 genomes]
rs9937129	0.81[ASN][1000 genomes]
rs9939368	0.84[ASN][1000 genomes]
rs9940599	0.81[ASN][1000 genomes]
rs9941289	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv428658	chr16:48438656-48587750	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1064323	chr16:48531171-48573066	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1060196	chr16:48531171-48578101	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8046716	NOD2	cis	cerebellum	SCAN
rs8046716	NKD1	cis	cerebellum	SCAN
rs8046716	N4BP1	cis	multi-tissue	Pritchard
rs8046716	PAPD5	cis	cerebellum	SCAN
rs8046716	C16orf78	cis	cerebellum	SCAN
rs8046716	LCE1B	trans	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48555800-48561000	Enhancers	Placenta	Placenta
2	chr16:48558000-48561000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:48558200-48561000	Flanking Bivalent TSS/Enh	HepG2	liver
4	chr16:48558600-48561200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:48559000-48561000	Enhancers	Colonic Mucosa	Colon
6	chr16:48559000-48561000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr16:48559200-48565600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:48559200-48571600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr16:48559400-48561200	Enhancers	Stomach Mucosa	stomach
10	chr16:48559600-48570400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:48560000-48561000	Enhancers	Hela-S3	cervix
12	chr16:48560000-48561200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:48560000-48561200	Enhancers	NHEK	skin
14	chr16:48560200-48561000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr16:48560200-48561000	Enhancers	Esophagus	oesophagus
16	chr16:48560200-48561200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr16:48560400-48561000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:48560600-48561000	Enhancers	Duodenum Mucosa	Duodenum
19	chr16:48560600-48561000	Enhancers	Fetal Intestine Large	intestine
20	chr16:48560600-48561000	Enhancers	Fetal Intestine Small	intestine
21	chr16:48560600-48561200	Enhancers	HMEC	breast
22	chr16:48560800-48561000	Enhancers	Spleen	Spleen
23	chr16:48560800-48565000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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