Variant report

Variant	rs1362406
Chromosome Location	chr16:46996557-46996558
allele	A/C
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	BACH1	chr16:46996550-46996915	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr16:46996213-46996850	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:46996259-46996670	GM12878	blood:	n/a	n/a
4	MAFF	chr16:46996540-46996907	K562	blood:	n/a	chr16:46996714-46996732
5	MAFF	chr16:46996555-46996873	HepG2	liver:	n/a	chr16:46996714-46996732
6	POLR2A	chr16:46996267-46996679	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46995915..47000347-chr16:47005610..47008323,5	MCF-7	breast:
2	chr16:46995618..46998469-chr16:46998701..47003267,4	MCF-7	breast:

Variant related genes	Relation type
DNAJA2	TF binding region
ENSG00000069345	Chromatin interaction
ENSG00000261173	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10459877	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11247542	0.94[EUR][1000 genomes]
rs11247543	0.81[EUR][1000 genomes]
rs11859515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445492	0.92[EUR][1000 genomes]
rs12447719	0.94[EUR][1000 genomes]
rs12596824	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12719759	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12925296	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1376734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551188	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1894886	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978336	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2058673	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341648	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35405784	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs4577108	0.94[EUR][1000 genomes]
rs4625742	0.86[EUR][1000 genomes]
rs4966781	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966794	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966795	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966800	0.94[EUR][1000 genomes]
rs4967664	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967696	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967724	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4967726	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4967727	0.84[AMR][1000 genomes]
rs4967739	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62059134	0.83[ASN][1000 genomes]
rs7189628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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]
rs7199379	0.94[EUR][1000 genomes]
rs7199772	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7202325	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203206	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046142	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047353	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8052160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054039	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.95[EUR][1000 genomes]
rs8058144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058714	0.80[EUR][1000 genomes]
rs8060193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9745921	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923192	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925290	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925525	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9927843	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1362406	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46970400-46999000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:46977600-47006200	Weak transcription	Stomach Mucosa	stomach
3	chr16:46987600-47003400	Strong transcription	Liver	Liver
4	chr16:46988000-47002800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr16:46988000-47003000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr16:46988000-47003200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:46988000-47003200	Strong transcription	Brain Germinal Matrix	brain
8	chr16:46988000-47004200	Strong transcription	Fetal Thymus	thymus
9	chr16:46988000-47004400	Strong transcription	Primary T cells from cord blood	blood
10	chr16:46988000-47005400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr16:46988000-47005400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:46988000-47005600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:46988000-47005800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr16:46988200-47005400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr16:46988400-47002400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr16:46988400-47004600	Strong transcription	Thymus	Thymus
17	chr16:46988400-47005200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr16:46988400-47005800	Strong transcription	Fetal Muscle Leg	muscle
19	chr16:46988400-47006000	Strong transcription	Placenta	Placenta
20	chr16:46988600-47002600	Strong transcription	NH-A	brain
21	chr16:46988600-47003200	Strong transcription	Dnd41	blood
22	chr16:46988600-47003400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr16:46988600-47004200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr16:46988600-47005200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr16:46988600-47005200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr16:46988600-47005400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr16:46988600-47005800	Strong transcription	Fetal Intestine Large	intestine
28	chr16:46988800-47004200	Strong transcription	Fetal Brain Female	brain
29	chr16:46990000-47005800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr16:46990600-47003600	Strong transcription	Spleen	Spleen
31	chr16:46990600-47005800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr16:46991000-47004200	Strong transcription	Lung	lung
33	chr16:46992200-46997800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr16:46993200-46997400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr16:46993800-46997800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr16:46994000-46997200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr16:46994000-46997200	Weak transcription	Aorta	Aorta
38	chr16:46994000-46997800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr16:46994000-47005200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr16:46994200-46997800	Weak transcription	Gastric	stomach
41	chr16:46994200-47005400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr16:46994200-47005800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr16:46994400-46998000	Weak transcription	Colonic Mucosa	Colon
44	chr16:46994400-46998200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr16:46994400-47005200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr16:46994600-46997800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr16:46995000-46996800	Genic enhancers	Primary monocytes fromperipheralblood	blood
48	chr16:46995000-46996800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr16:46995200-46996600	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr16:46995200-46997400	Weak transcription	Fetal Intestine Small	intestine

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