Variant report

Variant	rs17035902
Chromosome Location	chr12:104982103-104982104
allele	G/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	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	MYC	chr12:104982014-104982830	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr12:104982047-104982843	Hela-S3	cervix:	n/a	chr12:104982275-104982283
6	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
7	POLR2A	chr12:104982027-104982752	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr12:104981930-104982899	A549	lung:	n/a	chr12:104982541-104982555
9	SP1	chr12:104981810-104982928	A549	lung:	n/a	n/a
10	JUND	chr12:104981829-104983032	HCT-116	colon:	n/a	chr12:104982275-104982283
11	FOS	chr12:104982027-104982875	MCF10A-Er-Src	breast:	n/a	chr12:104982273-104982284 chr12:104982275-104982283
12	TCF12	chr12:104981879-104982930	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr12:104981988-104982694	SK-N-SH	brain:	n/a	n/a
14	MAX	chr12:104981922-104982933	A549	lung:	n/a	n/a
15	JUND	chr12:104981896-104982918	HCT-116	colon:	n/a	chr12:104982275-104982283
16	RFX5	chr12:104982059-104982662	Hela-S3	cervix:	n/a	n/a
17	FOSL1	chr12:104981892-104983122	HCT-116	colon:	n/a	chr12:104982275-104982283
18	POLR2A	chr12:104982091-104982753	HCT-116	colon:	n/a	n/a
19	RCOR1	chr12:104981843-104982835	Hela-S3	cervix:	n/a	n/a
20	FOS	chr12:104982055-104982812	HUVEC	blood vessel:	n/a	chr12:104982273-104982284 chr12:104982275-104982283
21	POLR2A	chr12:104982091-104982546	HUVEC	blood vessel:	n/a	n/a
22	SP1	chr12:104981858-104982972	HCT-116	colon:	n/a	n/a
23	FOS	chr12:104981875-104982851	MCF10A-Er-Src	breast:	n/a	chr12:104982273-104982284 chr12:104982275-104982283
24	FOS	chr12:104982089-104982868	MCF10A-Er-Src	breast:	n/a	chr12:104982273-104982284 chr12:104982275-104982283
25	CHD2	chr12:104981976-104982711	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr12:104982069-104982807	Hela-S3	cervix:	n/a	chr12:104982541-104982555
27	FOSL2	chr12:104982008-104982543	SK-N-SH	brain:	n/a	chr12:104982275-104982283
28	CEBPB	chr12:104981876-104982938	A549	lung:	n/a	n/a
29	JUND	chr12:104982091-104982762	A549	lung:	n/a	chr12:104982275-104982283
30	NR3C1	chr12:104982023-104982580	A549	lung:	n/a	n/a
31	FOXA2	chr12:104982089-104982652	A549	lung:	n/a	n/a
32	GATA3	chr12:104981835-104983039	A549	lung:	n/a	chr12:104982407-104982414
33	STAT3	chr12:104982093-104982850	MCF10A-Er-Src	breast:	n/a	n/a
34	SP1	chr12:104981844-104983353	A549	lung:	n/a	n/a
35	YY1	chr12:104982103-104982736	A549	lung:	n/a	n/a
36	SMC3	chr12:104982074-104982841	Hela-S3	cervix:	n/a	chr12:104982521-104982528
37	MAX	chr12:104982032-104982919	A549	lung:	n/a	n/a
38	EP300	chr12:104981859-104982904	A549	lung:	n/a	n/a
39	CEBPB	chr12:104981964-104982968	HCT-116	colon:	n/a	n/a
40	EP300	chr12:104981924-104982873	A549	lung:	n/a	n/a
41	ATF3	chr12:104981945-104982689	A549	lung:	n/a	n/a
42	STAT3	chr12:104982087-104982786	Hela-S3	cervix:	n/a	n/a
43	TCF12	chr12:104981775-104982884	A549	lung:	n/a	n/a
44	CEBPB	chr12:104982000-104982796	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr12:104981996-104982745	Hela-S3	cervix:	n/a	n/a
46	FOSL2	chr12:104981974-104982631	SK-N-SH	brain:	n/a	chr12:104982275-104982283
47	FOSL1	chr12:104981823-104983068	HCT-116	colon:	n/a	chr12:104982275-104982283
48	FOSL2	chr12:104981777-104983000	A549	lung:	n/a	chr12:104982275-104982283
49	TFAP2C	chr12:104981902-104982770	Hela-S3	cervix:	n/a	n/a
50	MAX	chr12:104982079-104982739	A549	lung:	n/a	n/a

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

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10778341	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861240	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861241	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861242	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861243	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861244	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861245	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861246	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861248	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112118	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112119	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112120	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112121	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112122	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112123	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112124	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112125	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112126	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112127	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11610583	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1529423	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1529424	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17813400	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];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61938575	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6539161	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];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301126	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7301450	0.94[EUR][1000 genomes]
rs7306538	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7306664	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73187418	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73187426	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73187427	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73187429	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7954025	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7954312	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7979531	0.95[AMR][1000 genomes];0.97[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17035902	SPIC	cis	cerebellum	SCAN
rs17035902	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104965400-104982200	Weak transcription	Left Ventricle	heart
2	chr12:104971000-104990600	Weak transcription	Lung	lung
3	chr12:104971600-104982200	Weak transcription	Right Atrium	heart
4	chr12:104972200-104989800	Weak transcription	Fetal Brain Male	brain
5	chr12:104973800-104990800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:104974400-104984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:104974600-104987600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:104974600-104988800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:104974600-104990600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:104975000-104982200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:104975000-104988800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr12:104975600-104988400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:104975600-104992000	Weak transcription	Gastric	stomach
14	chr12:104976000-104987800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:104976800-104996800	Weak transcription	Primary T cells from cord blood	blood
16	chr12:104977200-104982200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:104977200-104987200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:104977400-104982200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:104977800-104982200	Weak transcription	Thymus	Thymus
20	chr12:104978000-104989600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:104978400-104989600	Weak transcription	Primary B cells from cord blood	blood
22	chr12:104978600-104982200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:104979000-104986000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:104980000-104982400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:104980200-104982200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:104980200-104982200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:104980200-104989200	Weak transcription	Fetal Thymus	thymus
28	chr12:104980200-104989800	Weak transcription	Aorta	Aorta
29	chr12:104980200-104997600	Weak transcription	Esophagus	oesophagus
30	chr12:104980400-104982200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:104980600-104985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:104980600-104990600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:104980800-104982200	Weak transcription	Fetal Kidney	kidney
34	chr12:104980800-104982200	Weak transcription	GM12878-XiMat	blood
35	chr12:104980800-104982400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:104981000-104985400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:104981200-104982200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:104981400-104982800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:104981400-104988600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:104981600-104982800	Flanking Active TSS	HMEC	breast
41	chr12:104981800-104982600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:104981800-104982800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:104981800-104982800	Flanking Active TSS	Hela-S3	cervix
44	chr12:104981800-104983000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:104981800-104983000	Enhancers	NHLF	lung
46	chr12:104981800-104983200	Flanking Active TSS	NHEK	skin
47	chr12:104981800-104983400	Flanking Active TSS	A549	lung
48	chr12:104982000-104982200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:104982000-104982200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr12:104982000-104982200	Flanking Active TSS	HUVEC	blood vessel

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