Variant report

Variant	rs3767716
Chromosome Location	chr1:223936168-223936169
allele	C/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	POLR2A	chr1:223936046-223936267	HCT-116	colon:	n/a	n/a
2	FOS	chr1:223936030-223936211	MCF10A-Er-Src	breast:	n/a	n/a
3	FOSL2	chr1:223935698-223936405	A549	lung:	n/a	n/a
4	POLR2A	chr1:223934367-223937187	U87	brain:	n/a	n/a
5	POLR2A	chr1:223936100-223936589	GM12892	blood:	n/a	n/a
6	TCF12	chr1:223935446-223937415	A549	lung:	n/a	chr1:223935761-223935771
7	RCOR1	chr1:223934896-223937499	IMR90	lung:	n/a	n/a
8	FOSL2	chr1:223935749-223936315	A549	lung:	n/a	n/a
9	MAX	chr1:223935695-223937237	A549	lung:	n/a	chr1:223935767-223935777 chr1:223935751-223935761
10	POLR2A	chr1:223935571-223936236	K562	blood:	n/a	n/a
11	MAZ	chr1:223934794-223937231	IMR90	lung:	n/a	chr1:223935767-223935777 chr1:223935751-223935761
12	EP300	chr1:223935658-223936411	A549	lung:	n/a	chr1:223935752-223935768
13	POLR2A	chr1:223935939-223936650	IMR90	lung:	n/a	n/a
14	FOS	chr1:223935871-223936401	HUVEC	blood vessel:	n/a	n/a
15	SP1	chr1:223935624-223936457	A549	lung:	n/a	n/a
16	POLR2A	chr1:223934506-223937545	K562	blood:	n/a	n/a
17	MAX	chr1:223936111-223937071	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOS	chr1:223935795-223936264	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:223936118-223936246	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:223936132-223936415	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:223935791-223936423	PANC-1	pancreas:	n/a	n/a
22	MAFK	chr1:223936091-223936325	IMR90	lung:	n/a	n/a
23	POLR2A	chr1:223935639-223937214	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr1:223935361-223936798	K562	blood:	n/a	n/a
25	FOXA2	chr1:223935874-223936590	A549	lung:	n/a	n/a
26	CHD2	chr1:223936109-223937115	H1-hESC	embryonic stem cell:	n/a	n/a
27	TBL1XR1	chr1:223936133-223936326	GM12878	blood:	n/a	n/a
28	FOXA2	chr1:223935922-223936498	A549	lung:	n/a	n/a
29	MXI1	chr1:223935038-223937318	IMR90	lung:	n/a	n/a
30	JUND	chr1:223936107-223936217	K562	blood:	n/a	n/a
31	E2F6	chr1:223936127-223937242	H1-hESC	embryonic stem cell:	n/a	n/a
32	GATA2	chr1:223935827-223936278	HUVEC	blood vessel:	n/a	chr1:223936006-223936016 chr1:223936202-223936211 chr1:223935997-223936014 chr1:223936003-223936019 chr1:223936008-223936015 chr1:223936008-223936015 chr1:223936147-223936160 chr1:223936008-223936015
33	E2F6	chr1:223936138-223937261	A549	lung:	n/a	n/a
34	FOS	chr1:223936161-223936235	MCF10A-Er-Src	breast:	n/a	n/a
35	MAX	chr1:223935584-223937348	A549	lung:	n/a	chr1:223935767-223935777 chr1:223935751-223935761
36	FOXP2	chr1:223936108-223936398	PFSK-1	brain:	n/a	n/a
37	NFIC	chr1:223935567-223936256	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr1:223934529-223937422	A549	lung:	n/a	n/a
39	NR3C1	chr1:223935706-223936394	A549	lung:	n/a	chr1:223936201-223936210
40	POLR2A	chr1:223934361-223937268	U87	brain:	n/a	n/a
41	BATF	chr1:223936084-223936283	GM12878	blood:	n/a	chr1:223936201-223936212 chr1:223936202-223936212
42	RAD21	chr1:223936017-223937318	IMR90	lung:	n/a	n/a
43	CEBPB	chr1:223935623-223936433	A549	lung:	n/a	n/a
44	BATF	chr1:223936096-223936303	GM12878	blood:	n/a	chr1:223936201-223936212 chr1:223936202-223936212

No.	Distal block	Cell Line	Cell type
1	chr1:223935650..223937154-chr1:223966505..223968008,2	MCF-7	breast:
2	chr1:223884441..223887114-chr1:223935723..223937532,2	MCF-7	breast:
3	chr1:223887852..223890245-chr1:223935483..223937346,2	MCF-7	breast:
4	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:
5	chr1:223886106..223889532-chr1:223933715..223936535,3	K562	blood:
6	chr1:223898965..223904523-chr1:223935616..223939096,7	MCF-7	breast:
7	chr1:223884772..223887549-chr1:223936018..223938654,2	MCF-7	breast:
8	chr1:223899274..223906539-chr1:223934896..223938666,15	MCF-7	breast:

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10503144	0.82[EUR][1000 genomes]
rs10915702	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915707	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915715	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1153965	0.86[EUR][1000 genomes]
rs12059128	0.85[EUR][1000 genomes]
rs12059770	0.85[EUR][1000 genomes]
rs12060361	0.85[EUR][1000 genomes]
rs12066704	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12066829	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12066831	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12069561	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12070057	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12080250	0.87[EUR][1000 genomes]
rs12088254	0.83[EUR][1000 genomes]
rs12091841	0.85[EUR][1000 genomes]
rs1222134	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1222138	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1222140	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1222141	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1222142	0.84[EUR][1000 genomes]
rs12562109	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12563291	0.96[EUR][1000 genomes]
rs12563477	0.87[EUR][1000 genomes]
rs12563637	0.93[EUR][1000 genomes]
rs12563713	0.94[EUR][1000 genomes]
rs12565967	0.85[EUR][1000 genomes]
rs12566817	0.82[EUR][1000 genomes]
rs16842162	0.87[EUR][1000 genomes]
rs16842229	0.85[EUR][1000 genomes]
rs16842257	0.82[EUR][1000 genomes]
rs17597	0.96[EUR][1000 genomes]
rs17598	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17600	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28370043	0.81[EUR][1000 genomes]
rs28370069	0.92[EUR][1000 genomes]
rs28370073	0.85[EUR][1000 genomes]
rs28370074	0.85[EUR][1000 genomes]
rs28370088	0.85[EUR][1000 genomes]
rs28370159	0.83[EUR][1000 genomes]
rs28370170	0.87[EUR][1000 genomes]
rs34683843	0.85[EUR][1000 genomes]
rs36032024	0.82[EUR][1000 genomes]
rs3738373	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738374	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738375	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767717	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767718	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3885657	0.85[EUR][1000 genomes]
rs59248553	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59275322	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61823580	0.82[EUR][1000 genomes]
rs61823581	0.82[EUR][1000 genomes]
rs61823583	0.82[EUR][1000 genomes]
rs61823585	0.82[EUR][1000 genomes]
rs61823587	0.82[EUR][1000 genomes]
rs61823591	0.82[EUR][1000 genomes]
rs61824003	0.87[EUR][1000 genomes]
rs61824005	0.83[EUR][1000 genomes]
rs61824008	0.85[EUR][1000 genomes]
rs6604724	0.85[EUR][1000 genomes]
rs6604727	0.82[EUR][1000 genomes]
rs6604728	0.81[EUR][1000 genomes]
rs6604729	0.81[EUR][1000 genomes]
rs6658954	0.82[EUR][1000 genomes]
rs6665485	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669080	0.82[CEU][hapmap]
rs6674541	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674846	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678365	0.81[EUR][1000 genomes]
rs6682412	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6682964	0.85[EUR][1000 genomes]
rs6685557	0.85[EUR][1000 genomes]
rs6691315	0.85[EUR][1000 genomes]
rs6694960	0.85[EUR][1000 genomes]
rs6700366	0.81[EUR][1000 genomes]
rs7331	0.87[EUR][1000 genomes]
rs751609	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528455	0.81[EUR][1000 genomes]
rs7530328	0.85[EUR][1000 genomes]
rs7533551	0.85[EUR][1000 genomes]
rs7555226	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs898876	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898877	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:223928000-223936400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:223928400-223936200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:223930600-223936200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:223931200-223954800	Strong transcription	HMEC	breast
8	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:223932200-223936400	Genic enhancers	NHLF	lung
10	chr1:223932600-223936400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:223932800-223936200	Weak transcription	Primary B cells from cord blood	blood
12	chr1:223933000-223937000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:223933400-223936400	Weak transcription	Thymus	Thymus
14	chr1:223934400-223936400	Genic enhancers	Lung	lung
15	chr1:223934600-223936600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:223934600-223937000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:223934600-223937000	Genic enhancers	NHDF-Ad	bronchial
18	chr1:223934800-223936400	Genic enhancers	Fetal Muscle Leg	muscle
19	chr1:223934800-223936400	Genic enhancers	Fetal Stomach	stomach
20	chr1:223934800-223936600	Genic enhancers	NHEK	skin
21	chr1:223934800-223937000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:223934800-223937000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:223934800-223937400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:223935000-223936400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:223935000-223937000	Genic enhancers	Placenta Amnion	Placenta Amnion
26	chr1:223935200-223936200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:223935200-223936400	Weak transcription	Primary T cells from cord blood	blood
28	chr1:223935200-223936400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:223935200-223936400	Weak transcription	Psoas Muscle	Psoas
30	chr1:223935200-223936400	Enhancers	HUVEC	blood vessel
31	chr1:223935200-223936600	Enhancers	Pancreas	Pancrea
32	chr1:223935200-223936800	Genic enhancers	HSMM	muscle
33	chr1:223935200-223937000	Weak transcription	Hela-S3	cervix
34	chr1:223935200-223937200	Enhancers	Fetal Heart	heart
35	chr1:223935400-223936200	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr1:223935400-223936200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:223935400-223936200	Enhancers	Brain Anterior Caudate	brain
38	chr1:223935400-223936200	Enhancers	Duodenum Mucosa	Duodenum
39	chr1:223935400-223936400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:223935400-223936400	Genic enhancers	Fetal Intestine Small	intestine
41	chr1:223935400-223936400	Weak transcription	Fetal Kidney	kidney
42	chr1:223935400-223936400	Genic enhancers	Gastric	stomach
43	chr1:223935400-223936600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:223935400-223936800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:223935400-223937000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:223935400-223937000	Genic enhancers	Osteobl	bone
47	chr1:223935400-223937400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:223935400-223937400	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr1:223935600-223936200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:223935600-223936200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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