Variant report

Variant	rs12596824
Chromosome Location	chr16:47009860-47009861
allele	A/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	RELA	chr16:47009812-47010875	GM12891	blood:	n/a	chr16:47009981-47009990 chr16:47009981-47009990
2	FOXM1	chr16:47009839-47010517	GM12878	blood:	n/a	n/a
3	ATF2	chr16:47009802-47010383	GM12878	blood:	n/a	n/a
4	NFATC1	chr16:47009730-47010749	GM12878	blood:	n/a	n/a
5	NFIC	chr16:47009687-47010864	GM12878	blood:	n/a	n/a
6	ATF2	chr16:47009825-47010478	GM12878	blood:	n/a	n/a
7	STAT5A	chr16:47009831-47010318	GM12878	blood:	n/a	chr16:47010212-47010223
8	RELA	chr16:47009836-47010658	GM12878	blood:	n/a	chr16:47009981-47009990 chr16:47009981-47009990
9	RELA	chr16:47009845-47010732	GM10847	blood:	n/a	chr16:47009981-47009990 chr16:47009981-47009990
10	RUNX3	chr16:47009828-47010810	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:46963289..46964254-chr16:47009598..47010534,2	K562	blood:
2	chr16:47007838..47011337-chr16:47047601..47050592,3	MCF-7	breast:
3	chr16:47009479..47012393-chr16:47173213..47175154,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPT2-1	chr16:47007627-47010136	NONHSAT142273

Variant related genes	Relation type
DNAJA2	TF binding region
ENSG00000259983	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10459877	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11247542	0.97[EUR][1000 genomes]
rs11247543	0.83[EUR][1000 genomes]
rs11859515	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445492	0.94[EUR][1000 genomes]
rs12447719	0.97[EUR][1000 genomes]
rs12719759	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12925296	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1362406	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376734	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551188	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1894886	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978336	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2058673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341648	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35405784	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577108	0.97[EUR][1000 genomes]
rs4625742	0.89[EUR][1000 genomes]
rs4966781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966794	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966795	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966800	0.97[EUR][1000 genomes]
rs4967664	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967724	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4967727	0.84[AMR][1000 genomes]
rs4967739	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62059134	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7189628	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199379	0.97[EUR][1000 genomes]
rs7199772	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7202325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203206	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046142	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047353	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8052160	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054039	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8058144	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058714	0.83[EUR][1000 genomes]
rs8060193	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9745921	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923192	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925290	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925525	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9927843	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	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
4	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

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47008400-47010400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr16:47008600-47010000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr16:47008600-47010000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr16:47008600-47010200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr16:47008600-47010400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:47008600-47010400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:47008600-47010400	Weak transcription	Stomach Mucosa	stomach
8	chr16:47008600-47010600	Weak transcription	Pancreas	Pancrea
9	chr16:47008800-47010000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr16:47008800-47010000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr16:47008800-47010000	Weak transcription	Liver	Liver
12	chr16:47008800-47010000	Weak transcription	HepG2	liver
13	chr16:47008800-47010200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr16:47008800-47010200	Weak transcription	Hela-S3	cervix
15	chr16:47008800-47010200	Weak transcription	NHEK	skin
16	chr16:47008800-47010400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr16:47008800-47010400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr16:47008800-47010400	Weak transcription	HMEC	breast
19	chr16:47008800-47010400	Weak transcription	K562	blood
20	chr16:47008800-47010800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:47008800-47011600	Weak transcription	Brain Angular Gyrus	brain
22	chr16:47008800-47012800	Weak transcription	Fetal Muscle Leg	muscle
23	chr16:47008800-47015000	Weak transcription	Brain Substantia Nigra	brain
24	chr16:47009000-47010000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr16:47009000-47010000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr16:47009000-47010000	Weak transcription	A549	lung
27	chr16:47009000-47010200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr16:47009600-47010800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr16:47009600-47011200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr16:47009800-47011000	Flanking Active TSS	GM12878-XiMat	blood

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