Variant report

Variant	rs1696363
Chromosome Location	chr12:121345202-121345203
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	FOSL2	chr12:121345027-121345443	HepG2	liver:	n/a	chr12:121345254-121345261 chr12:121345252-121345261 chr12:121345249-121345260 chr12:121345251-121345263
2	JUND	chr12:121344950-121345396	HepG2	liver:	n/a	chr12:121345251-121345262 chr12:121345254-121345261 chr12:121345252-121345261 chr12:121345249-121345260 chr12:121345251-121345263
3	CTCF	chr12:121345200-121345350	NHLF	lung:	n/a	n/a
4	BHLHE40	chr12:121344907-121345224	HepG2	liver:	n/a	n/a
5	CTCF	chr12:121345060-121345210	AoAF	blood vessel:	n/a	n/a
6	CTCF	chr12:121345160-121345310	HEEpiC	esophagus:	n/a	n/a
7	FOS	chr12:121345103-121345378	MCF10A-Er-Src	breast:	n/a	chr12:121345254-121345261 chr12:121345252-121345261 chr12:121345249-121345260 chr12:121345251-121345263
8	E2F4	chr12:121345124-121345411	MCF10A-Er-Src	breast:	n/a	n/a
9	MAZ	chr12:121345120-121345264	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:121344965-121345357	MCF10A-Er-Src	breast:	n/a	n/a
11	MAFF	chr12:121345088-121345297	HepG2	liver:	n/a	n/a
12	USF2	chr12:121345177-121345309	Hela-S3	cervix:	n/a	n/a
13	FOS	chr12:121345061-121345415	MCF10A-Er-Src	breast:	n/a	chr12:121345254-121345261 chr12:121345252-121345261 chr12:121345249-121345260 chr12:121345251-121345263
14	STAT3	chr12:121345201-121345385	MCF10A-Er-Src	breast:	n/a	chr12:121345336-121345344
15	TEAD4	chr12:121344776-121345238	HepG2	liver:	n/a	n/a
16	MYC	chr12:121345115-121345389	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr12:121345069-121345423	MCF10A-Er-Src	breast:	n/a	chr12:121345254-121345261 chr12:121345252-121345261 chr12:121345249-121345260 chr12:121345251-121345263
18	RAD21	chr12:121345164-121345231	Hela-S3	cervix:	n/a	n/a
19	SMC3	chr12:121345099-121345295	HepG2	liver:	n/a	n/a
20	FOS	chr12:121345098-121345432	MCF10A-Er-Src	breast:	n/a	chr12:121345254-121345261 chr12:121345252-121345261 chr12:121345249-121345260 chr12:121345251-121345263
21	TBP	chr12:121345029-121345286	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121341147..121344429-chr12:121344566..121350516,5	K562	blood:
2	chr12:121336041..121337901-chr12:121343531..121346196,2	MCF-7	breast:

Variant related genes	Relation type
SPPL3	TF binding region
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1067742	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10774577	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849818	0.89[ASN][1000 genomes]
rs1105416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065286	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1151850	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1151851	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs1151852	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1151861	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1151863	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1151864	0.84[ASN][1000 genomes]
rs1168945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168954	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1696361	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718211	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732395	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732396	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732398	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732405	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2454729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649994	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2649995	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2649996	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701174	0.84[ASN][1000 genomes]
rs2701178	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2701181	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701182	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767938	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs482522	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap]
rs487310	0.89[CHB][hapmap]
rs487912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs491602	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs497273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs509152	0.84[ASW][hapmap]
rs532140	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap]
rs532703	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs538785	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs550349	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap]
rs551087	0.90[JPT][hapmap]
rs566994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs584001	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs586305	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap]
rs589699	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs594507	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs610578	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap]
rs618849	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs619679	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs628771	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs631168	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs633084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6553	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs662284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs662739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs674021	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap]
rs679833	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs683091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs683437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs688402	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs694303	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs7300722	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs791210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs791713	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv560448	chr12:121341477-121364324	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription 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	7 gene(s)	inside rSNPs	diseases
6	nsv560452	chr12:121341581-121357934	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv560453	chr12:121342186-121364324	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1696363	SPPL3	cis	Adipose Subcutaneous	GTEx
rs1696363	NOS1	cis	parietal	SCAN
rs1696363	P2RX4	cis	cerebellum	SCAN
rs1696363	SPPL3	cis	cerebellum	SCAN
rs1696363	UNQ1887	cis	Temporal Cortex	GTEx
rs1696363	SRRM4	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121342600-121345400	Weak transcription	Lung	lung
2	chr12:121342600-121345400	Weak transcription	Right Atrium	heart
3	chr12:121342600-121345800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:121342600-121345800	Enhancers	HMEC	breast
5	chr12:121342600-121346000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:121342600-121347600	Enhancers	Placenta	Placenta
7	chr12:121342800-121345800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:121342800-121346200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:121342800-121346600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:121342800-121347000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:121342800-121347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:121342800-121347400	Weak transcription	GM12878-XiMat	blood
13	chr12:121343000-121362800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:121343200-121347200	Weak transcription	Spleen	Spleen
15	chr12:121343600-121345800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr12:121343800-121347400	Enhancers	Esophagus	oesophagus
17	chr12:121344400-121345400	Weak transcription	Psoas Muscle	Psoas
18	chr12:121344400-121346000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:121344600-121346200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:121344800-121345600	Enhancers	Fetal Heart	heart
21	chr12:121344800-121345800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr12:121344800-121346200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:121344800-121346200	Enhancers	Hela-S3	cervix
24	chr12:121345000-121345400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:121345000-121345400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:121345000-121345400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr12:121345000-121345400	Flanking Active TSS	NHDF-Ad	bronchial
28	chr12:121345000-121345400	Flanking Active TSS	NHEK	skin
29	chr12:121345000-121345600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:121345000-121345600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:121345000-121345600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:121345000-121345600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:121345000-121345600	Enhancers	Placenta Amnion	Placenta Amnion
34	chr12:121345000-121345600	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr12:121345000-121345600	Enhancers	HSMM	muscle
36	chr12:121345000-121345800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:121345000-121345800	Enhancers	Aorta	Aorta
38	chr12:121345000-121345800	Enhancers	NH-A	brain
39	chr12:121345200-121345400	Enhancers	Osteobl	bone
40	chr12:121345200-121345600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:121345200-121345600	Enhancers	NHLF	lung
42	chr12:121345200-121345800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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