Variant report

Variant	rs17100619
Chromosome Location	chr12:65127852-65127853
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	USF2	chr12:65127672-65128188	Hela-S3	cervix:	n/a	n/a
2	NFIC	chr12:65127405-65128350	SK-N-SH	brain:	n/a	n/a
3	RFX5	chr12:65127666-65128058	Hela-S3	cervix:	n/a	n/a
4	MYC	chr12:65127664-65127994	MCF10A-Er-Src	breast:	n/a	n/a
5	TCF12	chr12:65127650-65128126	ECC-1	luminal epithelium:	n/a	chr12:65127831-65127838
6	POLR2A	chr12:65127514-65128064	U87	brain:	n/a	n/a
7	POLR2A	chr12:65127618-65128027	U87	brain:	n/a	n/a
8	TEAD4	chr12:65127689-65128122	HCT-116	colon:	n/a	n/a
9	SIN3AK20	chr12:65127592-65128158	HCT-116	colon:	n/a	n/a
10	MAFK	chr12:65127679-65128112	Hela-S3	cervix:	n/a	n/a
11	TCF12	chr12:65127442-65128370	SK-N-SH	brain:	n/a	chr12:65127831-65127838
12	FOSL2	chr12:65127619-65128074	SK-N-SH	brain:	n/a	n/a
13	TEAD4	chr12:65127616-65128194	ECC-1	luminal epithelium:	n/a	n/a
14	TCF12	chr12:65127498-65128419	SK-N-SH	brain:	n/a	chr12:65127831-65127838
15	MYC	chr12:65127780-65127895	MCF-7	breast:	n/a	n/a
16	GTF2F1	chr12:65127710-65128022	Hela-S3	cervix:	n/a	n/a
17	FOSL1	chr12:65127644-65128155	HCT-116	colon:	n/a	n/a
18	EP300	chr12:65127556-65128120	T-47D	breast:	n/a	chr12:65127569-65127576 chr12:65127609-65127618
19	POLR2A	chr12:65127763-65127977	HCT-116	colon:	n/a	n/a
20	STAT3	chr12:65127683-65128067	MCF10A-Er-Src	breast:	n/a	n/a
21	PRDM1	chr12:65127747-65128052	Hela-S3	cervix:	n/a	n/a
22	MAX	chr12:65127557-65128190	SK-N-SH	brain:	n/a	n/a
23	MAX	chr12:65127632-65128353	ECC-1	luminal epithelium:	n/a	n/a
24	FOS	chr12:65127684-65128064	MCF10A-Er-Src	breast:	n/a	n/a
25	NFIC	chr12:65127451-65128240	ECC-1	luminal epithelium:	n/a	n/a
26	MYC	chr12:65127690-65128064	MCF10A-Er-Src	breast:	n/a	n/a
27	MXI1	chr12:65127582-65127874	HepG2	liver:	n/a	n/a
28	TEAD4	chr12:65127547-65128471	ECC-1	luminal epithelium:	n/a	n/a
29	CEBPB	chr12:65127705-65128100	Hela-S3	cervix:	n/a	n/a
30	STAT3	chr12:65127688-65128054	MCF10A-Er-Src	breast:	n/a	n/a
31	ESR1	chr12:65127675-65128079	ECC-1	luminal epithelium:	n/a	n/a
32	EP300	chr12:65127456-65128234	SK-N-SH	brain:	n/a	chr12:65127569-65127576 chr12:65127609-65127618 chr12:65127510-65127520
33	MAX	chr12:65127646-65128060	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr12:65127679-65127991	Hela-S3	cervix:	n/a	n/a
35	MYC	chr12:65127813-65127939	HUVEC	blood vessel:	n/a	n/a
36	MXI1	chr12:65127642-65128155	Hela-S3	cervix:	n/a	n/a
37	PBX3	chr12:65127450-65128257	SK-N-SH	brain:	n/a	n/a
38	TEAD4	chr12:65127531-65128181	SK-N-SH	brain:	n/a	n/a
39	NFIC	chr12:65127527-65128243	ECC-1	luminal epithelium:	n/a	n/a
40	FOSL2	chr12:65127477-65128077	SK-N-SH	brain:	n/a	n/a
41	STAT3	chr12:65127737-65127995	MCF10A-Er-Src	breast:	n/a	n/a
42	FOSL1	chr12:65127577-65128158	HCT-116	colon:	n/a	n/a
43	MAX	chr12:65127502-65128101	MCF-7	breast:	n/a	n/a
44	EP300	chr12:65127648-65127936	SK-N-SH_RA	brain:	n/a	n/a
45	POLR2A	chr12:65127697-65127961	HCT-116	colon:	n/a	n/a
46	SP1	chr12:65127559-65128137	HCT-116	colon:	n/a	n/a
47	SMC3	chr12:65127689-65128024	Hela-S3	cervix:	n/a	n/a
48	RCOR1	chr12:65127677-65128033	Hela-S3	cervix:	n/a	n/a
49	STAT3	chr12:65127740-65127995	MCF10A-Er-Src	breast:	n/a	n/a
50	PBX3	chr12:65127379-65128383	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:65126610..65129376-chr12:65136546..65139386,2	MCF-7	breast:
2	chr12:65125246..65129476-chr12:65130060..65133197,5	MCF-7	breast:

Variant related genes	Relation type
GNS	TF binding region
ENSG00000135677	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17100621	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17100633	1.00[MEX][hapmap]
rs17100642	1.00[MEX][hapmap]
rs2230292	0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56953843	1.00[AMR][1000 genomes]
rs74098127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74098643	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv899209	chr12:65068686-65184236	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv899210	chr12:65076498-65184236	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17100619	TBC1D30	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65106400-65152600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:65110600-65138400	Weak transcription	Stomach Mucosa	stomach
3	chr12:65111600-65146800	Strong transcription	Fetal Intestine Large	intestine
4	chr12:65115000-65130000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:65115600-65132000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:65117000-65128200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:65117000-65129800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:65117000-65132800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:65117400-65129400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:65120800-65130000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:65121600-65139400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:65124200-65138200	Strong transcription	Fetal Stomach	stomach
13	chr12:65124400-65129200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:65124600-65128400	Weak transcription	Right Atrium	heart
15	chr12:65124600-65129400	Weak transcription	Fetal Kidney	kidney
16	chr12:65124800-65137200	Strong transcription	Fetal Intestine Small	intestine
17	chr12:65125000-65129000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:65125000-65129600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:65125000-65136400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:65125200-65128000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr12:65125200-65132800	Weak transcription	Small Intestine	intestine
22	chr12:65125200-65132800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:65125200-65152400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:65125400-65131400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:65125600-65144400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:65126400-65128400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:65126600-65128600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr12:65126600-65130400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:65126600-65131000	Strong transcription	Fetal Thymus	thymus
30	chr12:65126800-65129600	Genic enhancers	Fetal Muscle Leg	muscle
31	chr12:65126800-65134200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:65126800-65138400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:65126800-65147800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr12:65127000-65133400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr12:65127200-65128000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:65127200-65128000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
37	chr12:65127200-65128000	Strong transcription	GM12878-XiMat	blood
38	chr12:65127200-65128200	Enhancers	Aorta	Aorta
39	chr12:65127200-65128200	Enhancers	HUVEC	blood vessel
40	chr12:65127200-65128200	Enhancers	NHEK	skin
41	chr12:65127200-65128400	Genic enhancers	Brain Anterior Caudate	brain
42	chr12:65127200-65128400	Genic enhancers	Brain Cingulate Gyrus	brain
43	chr12:65127200-65128400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr12:65127200-65128400	Strong transcription	K562	blood
45	chr12:65127200-65128600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:65127200-65128600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr12:65127200-65128600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:65127200-65128600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:65127200-65128600	Enhancers	Hela-S3	cervix
50	chr12:65127200-65128600	Enhancers	HMEC	breast

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