Variant report

Variant	rs12716823
Chromosome Location	chr16:77226052-77226053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr16:77224265-77226878	IMR90	lung:	n/a	n/a
2	POLR2A	chr16:77223958-77226689	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr16:77223928-77228004	GM12878	blood:	n/a	n/a
4	MYC	chr16:77224335-77226093	K562	blood:	n/a	chr16:77225677-77225687
5	POLR2A	chr16:77224076-77226313	GM18505	blood:	n/a	n/a
6	MAX	chr16:77224190-77226083	Hela-S3	cervix:	n/a	chr16:77225677-77225687
7	POLR2A	chr16:77224403-77226633	IMR90	lung:	n/a	n/a
8	TBL1XR1	chr16:77225531-77226285	K562	blood:	n/a	n/a
9	POLR2A	chr16:77224003-77226764	GM12891	blood:	n/a	n/a
10	POLR2A	chr16:77224098-77226588	HepG2	liver:	n/a	n/a
11	POLR2A	chr16:77224149-77226116	K562	blood:	n/a	n/a
12	POLR2A	chr16:77222637-77230176	K562	blood:	n/a	n/a
13	POLR2A	chr16:77225558-77226175	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:77223988-77226457	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr16:77224144-77226204	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:77223931-77226612	GM12878	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:77223598..77226407-chr16:77245076..77246907,2	MCF-7	breast:
2	chr16:77223287..77227235-chr16:77231893..77237199,5	MCF-7	breast:
3	chr12:46121915..46124342-chr16:77224976..77226839,2	K562	blood:
4	chr16:77223216..77226884-chr16:77251990..77255920,6	MCF-7	breast:
5	chr16:75680522..75683233-chr16:77224728..77226496,3	MCF-7	breast:
6	chr16:75680135..75682966-chr16:77223241..77226200,3	MCF-7	breast:
7	chr16:77223534..77226455-chr16:77227601..77231752,9	MCF-7	breast:
8	chr1:200638562..200641266-chr16:77224293..77226737,2	MCF-7	breast:
9	chr16:77223627..77226316-chr16:77230976..77234622,5	MCF-7	breast:
10	chr16:77225300..77227094-chr16:77244120..77246217,2	MCF-7	breast:
11	chr16:77223923..77226639-chr16:77244818..77248823,8	K562	blood:
12	chr16:77224814..77227187-chr16:77245098..77247161,3	K562	blood:

No data

Variant related genes	Relation type
MON1B	TF binding region
ENSG00000189079	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000118197	Chromatin interaction
ENSG00000103111	Chromatin interaction
ENSG00000205078	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000226348	Chromatin interaction
ENSG00000260088	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10781982	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11149970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11149972	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11149975	0.83[ASN][1000 genomes]
rs11639911	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11649440	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12447059	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12448094	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2113282	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232504	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232509	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241415	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241416	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278045	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34143201	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35660173	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3743759	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743761	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3760004	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760005	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760006	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760007	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887893	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62049594	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62049596	0.95[ASN][1000 genomes]
rs6420403	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564404	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564405	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564406	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564407	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564408	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564414	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7185297	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7185889	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194408	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7195255	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202265	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204238	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7205119	1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047912	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8048285	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8052509	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8062063	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9923489	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9924160	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9924694	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9930201	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9930541	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939130	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9939212	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869201	chr16:76714549-77233646	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1057677	chr16:76861946-77230013	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1065343	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv542965	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
12	nsv906954	chr16:77197633-77227180	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	nsv906955	chr16:77202701-77227180	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
14	esv11803	chr16:77224589-77227011	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12716823	SYCE1L	cis	Artery Tibial	GTEx
rs12716823	MON1B	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77223200-77226200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr16:77223400-77226600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:77223600-77226200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr16:77223800-77226200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr16:77223800-77226600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr16:77224000-77226200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:77224000-77226200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:77224000-77226200	Active TSS	Fetal Intestine Large	intestine
9	chr16:77224000-77226200	Active TSS	Psoas Muscle	Psoas
10	chr16:77224000-77226200	Active TSS	Right Atrium	heart
11	chr16:77224000-77226200	Active TSS	NHDF-Ad	bronchial
12	chr16:77224000-77226400	Active TSS	Fetal Kidney	kidney
13	chr16:77224200-77226200	Active TSS	HSMMtube	muscle
14	chr16:77225200-77226200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr16:77225200-77226200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr16:77225200-77226400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:77225200-77226400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr16:77225200-77226400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr16:77225200-77226600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr16:77225400-77226200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr16:77225400-77226200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr16:77225400-77226200	Flanking Active TSS	Fetal Stomach	stomach
23	chr16:77225400-77226200	Flanking Active TSS	Fetal Thymus	thymus
24	chr16:77225400-77226200	Flanking Active TSS	Thymus	Thymus
25	chr16:77225400-77226200	Flanking Active TSS	HUVEC	blood vessel
26	chr16:77225400-77226200	Flanking Active TSS	Osteobl	bone
27	chr16:77225400-77226400	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr16:77225400-77226400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr16:77225400-77226400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr16:77225400-77226400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr16:77225400-77226400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr16:77225400-77226400	Flanking Active TSS	NHEK	skin
33	chr16:77225400-77226600	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr16:77225400-77226600	Flanking Active TSS	Fetal Lung	lung
35	chr16:77225400-77226600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr16:77225400-77226600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr16:77225400-77226800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr16:77225400-77226800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr16:77225400-77226800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr16:77225600-77226200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr16:77225600-77226200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr16:77225600-77226200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr16:77225600-77226200	Flanking Active TSS	HSMM	muscle
44	chr16:77225600-77226200	Flanking Active TSS	NH-A	brain
45	chr16:77225600-77226400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr16:77225600-77226400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr16:77225600-77226400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr16:77225600-77226400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr16:77225600-77226400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr16:77225600-77226400	Flanking Active TSS	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links