Variant report

Variant	rs2241416
Chromosome Location	chr16:77227180-77227181
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	chr16:77223928-77228004	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:77227112-77227965	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:77227111-77227244	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:77222637-77230176	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:77223287..77227235-chr16:77231893..77237199,5	MCF-7	breast:
2	chr16:77224814..77227187-chr16:77245098..77247161,3	K562	blood:

Variant related genes	Relation type
MON1B	TF binding region
ENSG00000205078	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10781982	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11149970	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11149972	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11149975	0.83[ASN][1000 genomes]
rs11639911	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11649440	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12447059	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12448094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12716823	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2232504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232509	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];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241415	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34143201	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35660173	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3743759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3760004	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760005	0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760006	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887893	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62049594	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62049596	0.95[ASN][1000 genomes]
rs6420403	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564405	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564406	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564407	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564408	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564409	1.00[CHB][hapmap]
rs6564414	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7185297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7185889	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194408	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7195255	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202265	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204238	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7205119	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047912	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8048285	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8052509	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8062063	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9923489	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9924160	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9924694	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9930201	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9930541	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939130	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9939212	0.87[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	nsv523187	chr16:77227180-77229657	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2241416	SYCE1L	cis	Artery Tibial	GTEx
rs2241416	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	chr16:77225800-77227200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:77225800-77227200	Weak transcription	Esophagus	oesophagus
3	chr16:77225800-77227200	Weak transcription	Placenta	Placenta
4	chr16:77225800-77227200	Weak transcription	Lung	lung
5	chr16:77225800-77227400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:77225800-77227400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr16:77225800-77227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:77225800-77227400	Weak transcription	Aorta	Aorta
9	chr16:77225800-77227400	Enhancers	Spleen	Spleen
10	chr16:77225800-77228000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr16:77226000-77227200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr16:77226000-77227200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr16:77226000-77227200	Weak transcription	Ovary	ovary
14	chr16:77226000-77227400	Enhancers	Small Intestine	intestine
15	chr16:77226000-77228200	Transcr. at gene 5' and 3'	Dnd41	blood
16	chr16:77226200-77227200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr16:77226200-77227400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr16:77226200-77227400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr16:77226200-77227800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
20	chr16:77226200-77228600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
21	chr16:77226200-77229200	Weak transcription	HSMMtube	muscle
22	chr16:77226200-77233000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr16:77226200-77240400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr16:77226400-77227200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr16:77226400-77227200	Weak transcription	Fetal Intestine Small	intestine
26	chr16:77226400-77227200	Enhancers	Fetal Kidney	kidney
27	chr16:77226400-77227200	Enhancers	Right Ventricle	heart
28	chr16:77226400-77227600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr16:77226400-77228000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr16:77226400-77228000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr16:77226400-77228000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr16:77226400-77228800	Weak transcription	Osteobl	bone
33	chr16:77226400-77229000	Weak transcription	NH-A	brain
34	chr16:77226400-77229600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr16:77226400-77240200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr16:77226600-77227200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr16:77226600-77227200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr16:77226600-77227200	Enhancers	Brain Germinal Matrix	brain
39	chr16:77226600-77227200	Weak transcription	Brain Substantia Nigra	brain
40	chr16:77226600-77227200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr16:77226600-77227200	Weak transcription	Fetal Intestine Large	intestine
42	chr16:77226600-77227200	Weak transcription	Fetal Stomach	stomach
43	chr16:77226600-77227200	Weak transcription	Left Ventricle	heart
44	chr16:77226600-77227200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr16:77226600-77227200	Enhancers	Hela-S3	cervix
46	chr16:77226600-77227400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr16:77226600-77227400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr16:77226600-77227400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr16:77226600-77227400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr16:77226600-77227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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