Variant report

Variant	rs17103246
Chromosome Location	chr14:35834525-35834526
allele	C/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	JUND	chr14:35834434-35835289	SK-N-SH	brain:	n/a	chr14:35834850-35834861 chr14:35834851-35834860 chr14:35834867-35834877
2	MAX	chr14:35834441-35835086	K562	blood:	n/a	n/a
3	GTF2F1	chr14:35834516-35835085	Hela-S3	cervix:	n/a	n/a
4	MAFF	chr14:35834431-35835076	HepG2	liver:	n/a	n/a
5	MTA3	chr14:35834377-35835086	GM12878	blood:	n/a	n/a
6	MAZ	chr14:35834519-35835308	K562	blood:	n/a	n/a
7	MAFK	chr14:35834408-35835227	HepG2	liver:	n/a	n/a
8	NFIC	chr14:35834374-35835283	HepG2	liver:	n/a	n/a
9	BHLHE40	chr14:35834468-35835502	K562	blood:	n/a	n/a
10	EP300	chr14:35834495-35835169	HepG2	liver:	n/a	chr14:35835092-35835106
11	USF1	chr14:35834285-35835246	HCT-116	colon:	n/a	chr14:35834441-35834452
12	BHLHE40	chr14:35834439-35835076	HepG2	liver:	n/a	n/a
13	JUN	chr14:35834275-35837620	K562	blood:	n/a	chr14:35835528-35835536 chr14:35834851-35834860 chr14:35836358-35836366 chr14:35835528-35835536 chr14:35835529-35835536 chr14:35836354-35836365 chr14:35834867-35834877
14	MAX	chr14:35834305-35835171	HepG2	liver:	n/a	n/a
15	EP300	chr14:35834298-35835233	HepG2	liver:	n/a	chr14:35835092-35835106
16	MBD4	chr14:35834458-35835273	HepG2	liver:	n/a	n/a
17	FOSL2	chr14:35834500-35835218	HepG2	liver:	n/a	chr14:35834851-35834860 chr14:35834849-35834860 chr14:35834867-35834877
18	STAT3	chr14:35834469-35835176	MCF10A-Er-Src	breast:	n/a	chr14:35835050-35835059 chr14:35835045-35835065 chr14:35835090-35835101 chr14:35835051-35835060
19	MAX	chr14:35834424-35835070	NB4	blood:	n/a	n/a
20	EP300	chr14:35834474-35835085	HepG2	liver:	n/a	n/a
21	FOSL2	chr14:35834468-35835166	A549	lung:	n/a	chr14:35834851-35834860 chr14:35834849-35834860 chr14:35834867-35834877
22	FOS	chr14:35834442-35835156	MCF10A-Er-Src	breast:	n/a	chr14:35834851-35834860 chr14:35834867-35834877 chr14:35834850-35834861
23	STAT3	chr14:35834255-35835224	MCF10A-Er-Src	breast:	n/a	chr14:35835050-35835059 chr14:35835045-35835065 chr14:35835090-35835101 chr14:35835051-35835060
24	JUND	chr14:35834473-35835138	HepG2	liver:	n/a	chr14:35834850-35834861 chr14:35834851-35834860 chr14:35834867-35834877
25	JUND	chr14:35834499-35835095	Hela-S3	cervix:	n/a	chr14:35834850-35834861 chr14:35834851-35834860 chr14:35834867-35834877
26	POLR2A	chr14:35834313-35835788	U87	brain:	n/a	n/a
27	USF1	chr14:35834233-35834613	A549	lung:	n/a	chr14:35834441-35834452
28	MAX	chr14:35834197-35836101	HepG2	liver:	n/a	chr14:35835527-35835536
29	POLR2A	chr14:35834440-35837595	K562	blood:	n/a	n/a
30	SMC3	chr14:35834523-35835090	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr14:35834383-35835065	U87	brain:	n/a	n/a
32	RFX5	chr14:35834438-35835035	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr14:35834351-35835782	U87	brain:	n/a	n/a
34	MAX	chr14:35834287-35835329	HCT-116	colon:	n/a	n/a
35	SMARCC1	chr14:35834433-35835438	Hela-S3	cervix:	n/a	chr14:35834851-35834860
36	MAX	chr14:35834469-35835080	Hela-S3	cervix:	n/a	n/a
37	MAX	chr14:35834276-35835329	A549	lung:	n/a	n/a
38	MAFK	chr14:35834457-35835034	IMR90	lung:	n/a	n/a
39	USF1	chr14:35834296-35834561	HepG2	liver:	n/a	chr14:35834441-35834452
40	MXI1	chr14:35834474-35835122	HepG2	liver:	n/a	n/a
41	FOSL2	chr14:35834436-35835171	HepG2	liver:	n/a	chr14:35834851-35834860 chr14:35834849-35834860 chr14:35834867-35834877
42	MYBL2	chr14:35834100-35835224	HepG2	liver:	n/a	n/a
43	POLR2A	chr14:35834458-35835065	U87	brain:	n/a	n/a
44	CHD2	chr14:35834391-35834804	HepG2	liver:	n/a	n/a
45	SMARCB1	chr14:35834395-35836392	Hela-S3	cervix:	n/a	chr14:35834851-35834860
46	USF2	chr14:35834329-35835074	Hela-S3	cervix:	n/a	n/a
47	MAZ	chr14:35834181-35836269	IMR90	lung:	n/a	chr14:35835527-35835536

No.	Distal block	Cell Line	Cell type
1	chr14:35816577..35819351-chr14:35832841..35834841,2	K562	blood:
2	chr14:35834445..35839728-chr14:35850287..35856081,6	K562	blood:
3	chr14:35832015..35837880-chr14:35867331..35875279,15	K562	blood:
4	chr14:35821826..35833396-chr14:35833928..35840799,21	K562	blood:
5	chr14:35761614..35764239-chr14:35833257..35835376,2	K562	blood:
6	chr14:35833474..35838463-chr14:35839143..35843538,8	K562	blood:
7	chr14:35833202..35845291-chr14:35869974..35876968,23	K562	blood:
8	chr14:35761154..35763543-chr14:35833265..35835694,2	MCF-7	breast:
9	chr14:35825567..35827487-chr14:35834461..35837123,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258860	TF binding region
ENSG00000100902	Chromatin interaction
ENSG00000100906	Chromatin interaction
ENSG00000258860	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1073597	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11156883	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11621391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091835	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17103226	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs17103240	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17103242	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17103255	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103257	0.83[CHB][hapmap]
rs4272943	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs59618010	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS 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 target site	50 gene(s)	inside rSNPs	diseases
2	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
3	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
4	esv1829386	chr14:35789740-35845927	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv518090	chr14:35802483-35840241	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv528501	chr14:35825436-35840678	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17103246	KIAA0391	Cis_1M	lymphoblastoid	RTeQTL
rs17103246	PPP2R3C	cis	Whole Blood	GTEx
rs17103246	PPP2R3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35821600-35843800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:35822400-35834600	Weak transcription	Gastric	stomach
3	chr14:35822600-35836400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:35825600-35835200	Weak transcription	Aorta	Aorta
5	chr14:35827600-35836200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:35830600-35836200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr14:35831600-35837800	Enhancers	Osteobl	bone
8	chr14:35831600-35839000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr14:35831600-35839400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr14:35831800-35838000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:35832000-35836600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr14:35832400-35834600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:35832400-35834800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr14:35832400-35836000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr14:35832400-35836000	Weak transcription	Liver	Liver
16	chr14:35832800-35836400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr14:35833000-35836400	Weak transcription	Fetal Lung	lung
18	chr14:35833000-35837000	Weak transcription	Fetal Stomach	stomach
19	chr14:35833400-35834600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr14:35833400-35836600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr14:35833400-35838000	Enhancers	Fetal Intestine Small	intestine
22	chr14:35833400-35839200	Enhancers	Placenta	Placenta
23	chr14:35833600-35837600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr14:35834000-35834600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:35834000-35837600	Enhancers	Fetal Intestine Large	intestine
26	chr14:35834200-35835400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr14:35834200-35835400	Enhancers	NHEK	skin
28	chr14:35834200-35835600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:35834200-35835800	Enhancers	HMEC	breast
30	chr14:35834200-35835800	Enhancers	HUVEC	blood vessel
31	chr14:35834200-35836200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr14:35834200-35836200	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr14:35834200-35836400	Enhancers	K562	blood
34	chr14:35834200-35837200	Enhancers	Fetal Thymus	thymus
35	chr14:35834200-35837400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:35834200-35837400	Enhancers	Lung	lung
37	chr14:35834200-35837800	Enhancers	Primary T cells fromperipheralblood	blood
38	chr14:35834200-35837800	Enhancers	Spleen	Spleen
39	chr14:35834200-35838200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr14:35834200-35838400	Enhancers	NHLF	lung
41	chr14:35834200-35838600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:35834200-35838600	Enhancers	HSMMtube	muscle
43	chr14:35834200-35838600	Enhancers	NH-A	brain
44	chr14:35834200-35839400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr14:35834200-35839400	Enhancers	Stomach Smooth Muscle	stomach
46	chr14:35834200-35840000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr14:35834200-35840200	Enhancers	Primary hematopoietic stem cells	blood
48	chr14:35834400-35834600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr14:35834400-35834800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr14:35834400-35834800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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