Variant report

Variant	rs1650131
Chromosome Location	chr12:104982258-104982259
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	chr12:104982018-104982440	U87	brain:	n/a	n/a
2	POLR2A	chr12:104981910-104982789	HUVEC	blood vessel:	n/a	n/a
3	REST	chr12:104981860-104982745	A549	lung:	n/a	n/a
4	MAX	chr12:104982179-104982736	Hela-S3	cervix:	n/a	n/a
5	MYC	chr12:104982014-104982830	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr12:104982047-104982843	Hela-S3	cervix:	n/a	chr12:104982275-104982283
7	RAD21	chr12:104982192-104982613	IMR90	lung:	n/a	chr12:104982541-104982555
8	TFAP2A	chr12:104981884-104982770	Hela-S3	cervix:	n/a	chr12:104982365-104982375 chr12:104982557-104982571 chr12:104982365-104982375 chr12:104982542-104982557 chr12:104982557-104982571 chr12:104982365-104982375 chr12:104982365-104982375
9	POLR2A	chr12:104982027-104982752	Hela-S3	cervix:	n/a	n/a
10	RAD21	chr12:104981930-104982899	A549	lung:	n/a	chr12:104982541-104982555
11	SP1	chr12:104981810-104982928	A549	lung:	n/a	n/a
12	JUND	chr12:104981829-104983032	HCT-116	colon:	n/a	chr12:104982275-104982283
13	FOS	chr12:104982027-104982875	MCF10A-Er-Src	breast:	n/a	chr12:104982273-104982284 chr12:104982275-104982283
14	TCF12	chr12:104981879-104982930	SK-N-SH	brain:	n/a	n/a
15	STAT3	chr12:104982139-104983009	MCF10A-Er-Src	breast:	n/a	n/a
16	MAZ	chr12:104982211-104982634	Hela-S3	cervix:	n/a	n/a
17	TCF12	chr12:104981988-104982694	SK-N-SH	brain:	n/a	n/a
18	TAF1	chr12:104982112-104982437	Hela-S3	cervix:	n/a	n/a
19	MAX	chr12:104981922-104982933	A549	lung:	n/a	n/a
20	JUND	chr12:104981896-104982918	HCT-116	colon:	n/a	chr12:104982275-104982283
21	RFX5	chr12:104982059-104982662	Hela-S3	cervix:	n/a	n/a
22	FOSL1	chr12:104981892-104983122	HCT-116	colon:	n/a	chr12:104982275-104982283
23	POLR2A	chr12:104982091-104982753	HCT-116	colon:	n/a	n/a
24	RCOR1	chr12:104981843-104982835	Hela-S3	cervix:	n/a	n/a
25	FOS	chr12:104982055-104982812	HUVEC	blood vessel:	n/a	chr12:104982273-104982284 chr12:104982275-104982283
26	POLR2A	chr12:104982091-104982546	HUVEC	blood vessel:	n/a	n/a
27	SP1	chr12:104981858-104982972	HCT-116	colon:	n/a	n/a
28	POLR2A	chr12:104982169-104982664	Hela-S3	cervix:	n/a	n/a
29	JUND	chr12:104982149-104982759	A549	lung:	n/a	chr12:104982275-104982283
30	FOS	chr12:104981875-104982851	MCF10A-Er-Src	breast:	n/a	chr12:104982273-104982284 chr12:104982275-104982283
31	FOS	chr12:104982089-104982868	MCF10A-Er-Src	breast:	n/a	chr12:104982273-104982284 chr12:104982275-104982283
32	ZKSCAN1	chr12:104982249-104982690	Hela-S3	cervix:	n/a	n/a
33	CHD2	chr12:104981976-104982711	Hela-S3	cervix:	n/a	n/a
34	E2F4	chr12:104982141-104982503	MCF10A-Er-Src	breast:	n/a	chr12:104982304-104982315 chr12:104982308-104982315
35	RAD21	chr12:104982069-104982807	Hela-S3	cervix:	n/a	chr12:104982541-104982555
36	FOSL2	chr12:104982008-104982543	SK-N-SH	brain:	n/a	chr12:104982275-104982283
37	CEBPB	chr12:104981876-104982938	A549	lung:	n/a	n/a
38	JUND	chr12:104982091-104982762	A549	lung:	n/a	chr12:104982275-104982283
39	NR3C1	chr12:104982023-104982580	A549	lung:	n/a	n/a
40	FOXA2	chr12:104982089-104982652	A549	lung:	n/a	n/a
41	GATA3	chr12:104981835-104983039	A549	lung:	n/a	chr12:104982407-104982414
42	TCF7L2	chr12:104982126-104982718	Hela-S3	cervix:	n/a	n/a
43	STAT3	chr12:104982093-104982850	MCF10A-Er-Src	breast:	n/a	n/a
44	SP1	chr12:104981844-104983353	A549	lung:	n/a	n/a
45	YY1	chr12:104982103-104982736	A549	lung:	n/a	n/a
46	SMC3	chr12:104982074-104982841	Hela-S3	cervix:	n/a	chr12:104982521-104982528
47	CEBPB	chr12:104982200-104982740	A549	lung:	n/a	n/a
48	MAX	chr12:104982032-104982919	A549	lung:	n/a	n/a
49	EP300	chr12:104981859-104982904	A549	lung:	n/a	n/a
50	CEBPB	chr12:104981964-104982968	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
CHST11	TF binding region
MIR3922	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1615960	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1650129	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650130	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650134	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1650138	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1650140	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1650141	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1650143	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1704885	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1704887	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1704892	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1704893	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1704894	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1704895	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1704896	0.92[EUR][1000 genomes]
rs313320	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs313321	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs313322	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs313323	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104971000-104990600	Weak transcription	Lung	lung
2	chr12:104972200-104989800	Weak transcription	Fetal Brain Male	brain
3	chr12:104973800-104990800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:104974400-104984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:104974600-104987600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:104974600-104988800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:104974600-104990600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:104975000-104988800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:104975600-104988400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:104975600-104992000	Weak transcription	Gastric	stomach
11	chr12:104976000-104987800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:104976800-104996800	Weak transcription	Primary T cells from cord blood	blood
13	chr12:104977200-104987200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:104978000-104989600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:104978400-104989600	Weak transcription	Primary B cells from cord blood	blood
16	chr12:104979000-104986000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:104980000-104982400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:104980200-104989200	Weak transcription	Fetal Thymus	thymus
19	chr12:104980200-104989800	Weak transcription	Aorta	Aorta
20	chr12:104980200-104997600	Weak transcription	Esophagus	oesophagus
21	chr12:104980600-104985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:104980600-104990600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:104980800-104982400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr12:104981000-104985400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:104981400-104982800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:104981400-104988600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:104981600-104982800	Flanking Active TSS	HMEC	breast
28	chr12:104981800-104982600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:104981800-104982800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:104981800-104982800	Flanking Active TSS	Hela-S3	cervix
31	chr12:104981800-104983000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:104981800-104983000	Enhancers	NHLF	lung
33	chr12:104981800-104983200	Flanking Active TSS	NHEK	skin
34	chr12:104981800-104983400	Flanking Active TSS	A549	lung
35	chr12:104982000-104982400	Enhancers	Fetal Heart	heart
36	chr12:104982000-104982600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:104982000-104982600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:104982000-104982600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:104982000-104982600	Flanking Active TSS	NH-A	brain
40	chr12:104982000-104982800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:104982000-104982800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:104982000-104982800	Genic enhancers	Dnd41	blood
43	chr12:104982000-104982800	Enhancers	HSMM	muscle
44	chr12:104982000-104982800	Enhancers	HSMMtube	muscle
45	chr12:104982000-104983000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:104982000-104983000	Enhancers	Placenta	Placenta
47	chr12:104982000-104983600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:104982000-104985400	Enhancers	K562	blood
49	chr12:104982200-104982400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr12:104982200-104982400	Strong transcription	Thymus	Thymus

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