Variant report

Variant	rs11051551
Chromosome Location	chr12:31885994-31885995
allele	A/C
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	REST	chr12:31885896-31886162	SK-N-SH	brain:	n/a	n/a
2	TEAD4	chr12:31885728-31886521	HCT-116	colon:	n/a	n/a
3	FOS	chr12:31885788-31886224	Hela-S3	cervix:	n/a	chr12:31885991-31885999 chr12:31885991-31885999 chr12:31886005-31886016 chr12:31885984-31885995 chr12:31885923-31885932 chr12:31885989-31886000 chr12:31885992-31885999
4	RAD21	chr12:31885561-31886532	HCT-116	colon:	n/a	n/a
5	CEBPB	chr12:31885149-31886232	IMR90	lung:	n/a	chr12:31885294-31885305
6	POLR2A	chr12:31885894-31886343	HCT-116	colon:	n/a	n/a
7	UBTF	chr12:31885741-31886256	K562	blood:	n/a	n/a
8	EP300	chr12:31885911-31886448	GM12878	blood:	n/a	chr12:31885990-31885999
9	ZNF384	chr12:31885876-31886228	K562	blood:	n/a	n/a
10	CEBPB	chr12:31885792-31886314	MCF-7	breast:	n/a	n/a
11	STAT3	chr12:31885757-31886426	GM12878	blood:	n/a	chr12:31885874-31885881
12	TFAP2C	chr12:31885933-31886420	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr12:31885862-31886371	MCF10A-Er-Src	breast:	n/a	chr12:31885874-31885881
14	MAX	chr12:31885929-31886249	H1-hESC	embryonic stem cell:	n/a	n/a
15	CREB1	chr12:31885865-31886458	H1-hESC	embryonic stem cell:	n/a	n/a
16	FOS	chr12:31885705-31887060	MCF10A-Er-Src	breast:	n/a	chr12:31885991-31885999 chr12:31885991-31885999 chr12:31886005-31886016 chr12:31885984-31885995 chr12:31885923-31885932 chr12:31885989-31886000 chr12:31885992-31885999
17	CEBPB	chr12:31885007-31886497	A549	lung:	n/a	chr12:31885294-31885305
18	POLR2A	chr12:31885758-31886438	Hela-S3	cervix:	n/a	n/a
19	TCF7L2	chr12:31885829-31886430	HCT-116	colon:	n/a	n/a
20	JUN	chr12:31885715-31886337	Hela-S3	cervix:	n/a	chr12:31885991-31885999 chr12:31885991-31885999 chr12:31885984-31885995 chr12:31885923-31885932 chr12:31885992-31885999
21	CEBPB	chr12:31885139-31886412	Hela-S3	cervix:	n/a	chr12:31885294-31885305
22	RAD21	chr12:31885859-31886493	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr12:31885573-31886474	HCT-116	colon:	n/a	n/a
24	TCF12	chr12:31885489-31887228	A549	lung:	n/a	n/a
25	MAFK	chr12:31885869-31886176	HepG2	liver:	n/a	n/a
26	MYC	chr12:31885879-31886190	K562	blood:	n/a	n/a
27	CEBPB	chr12:31885427-31886563	HCT-116	colon:	n/a	n/a
28	POLR2A	chr12:31885863-31886280	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAZ	chr12:31885914-31886189	Hela-S3	cervix:	n/a	n/a
30	TEAD4	chr12:31885622-31886336	K562	blood:	n/a	n/a
31	JUND	chr12:31885658-31886340	MCF-7	breast:	n/a	chr12:31885991-31885999 chr12:31886005-31886016 chr12:31885991-31885999 chr12:31885989-31886000 chr12:31885984-31885995 chr12:31885923-31885932 chr12:31885992-31885999
32	POLR2A	chr12:31885860-31886457	Hela-S3	cervix:	n/a	n/a
33	RXRA	chr12:31885787-31886329	SK-N-SH	brain:	n/a	n/a
34	JUND	chr12:31885847-31886138	HepG2	liver:	n/a	chr12:31885991-31885999 chr12:31886005-31886016 chr12:31885991-31885999 chr12:31885989-31886000 chr12:31885984-31885995 chr12:31885923-31885932 chr12:31885992-31885999
35	SIN3AK20	chr12:31885672-31886485	HCT-116	colon:	n/a	n/a
36	GABPA	chr12:31885754-31886391	A549	lung:	n/a	n/a
37	STAT3	chr12:31885886-31886326	MCF10A-Er-Src	breast:	n/a	n/a
38	SP1	chr12:31885681-31887145	A549	lung:	n/a	n/a
39	JUN	chr12:31883565-31886531	K562	blood:	n/a	chr12:31885991-31885999 chr12:31885991-31885999 chr12:31885984-31885995 chr12:31885923-31885932 chr12:31885992-31885999
40	EP300	chr12:31885577-31887220	ECC-1	luminal epithelium:	n/a	chr12:31885990-31885999
41	BACH1	chr12:31885798-31886420	H1-hESC	embryonic stem cell:	n/a	n/a
42	TEAD4	chr12:31885844-31886252	H1-hESC	embryonic stem cell:	n/a	n/a
43	NFIC	chr12:31885751-31886536	GM12878	blood:	n/a	n/a
44	STAT5A	chr12:31885900-31886501	GM12878	blood:	n/a	n/a
45	SETDB1	chr12:31885716-31886224	U2OS	brain:	n/a	n/a
46	SMC3	chr12:31885809-31886244	Hela-S3	cervix:	n/a	n/a
47	YY1	chr12:31885867-31886356	H1-hESC	embryonic stem cell:	n/a	n/a
48	FOS	chr12:31885776-31886984	MCF10A-Er-Src	breast:	n/a	chr12:31885991-31885999 chr12:31885991-31885999 chr12:31886005-31886016 chr12:31885984-31885995 chr12:31885923-31885932 chr12:31885989-31886000 chr12:31885992-31885999
49	STAT5A	chr12:31885658-31886290	K562	blood:	n/a	chr12:31885874-31885881
50	TCF12	chr12:31885642-31886347	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31878269..31883010-chr12:31884108..31887220,4	MCF-7	breast:
2	chr12:31884351..31886609-chr12:31902358..31904418,2	MCF-7	breast:
3	chr12:31885987..31887663-chr12:31893396..31895350,2	K562	blood:
4	chr12:31885898..31889640-chr12:32111582..32115997,5	K562	blood:
5	chr12:31880350..31888706-chr12:31898122..31903847,15	K562	blood:
6	chr12:31885885..31887666-chr12:31889660..31891228,2	MCF-7	breast:
7	chr12:31885818..31888336-chr12:32049032..32051077,2	K562	blood:
8	chr12:31885928..31888449-chr12:32111582..32113888,2	K562	blood:
9	chr12:31881279..31883605-chr12:31884352..31886662,3	MCF-7	breast:

Variant related genes	Relation type
AMN1	TF binding region
ENSG00000244436	Chromatin interaction
ENSG00000174718	Chromatin interaction
ENSG00000151743	Chromatin interaction
ENSG00000256843	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10843992	0.88[CHB][hapmap]
rs11051514	0.88[CHB][hapmap]
rs11051515	0.88[CHB][hapmap]
rs11051516	0.88[CHB][hapmap]
rs11051517	0.87[CHB][hapmap]
rs11051519	0.91[AMR][1000 genomes]
rs11051522	0.92[MEX][hapmap]
rs11051536	1.00[CHB][hapmap]
rs11051537	0.93[AMR][1000 genomes]
rs11051538	1.00[CHB][hapmap]
rs11051540	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs11051547	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap]
rs11051549	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes]
rs4931536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes]
rs4931547	0.96[AMR][1000 genomes]
rs61932065	0.96[AMR][1000 genomes]
rs61932066	0.86[EUR][1000 genomes]
rs61932089	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers 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 target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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 target site	24 gene(s)	inside rSNPs	diseases
6	nsv898967	chr12:31858031-31899475	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2422415	chr12:31863360-31930722	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv1045464	chr12:31869888-32183792	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv541447	chr12:31869888-32183792	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
13	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv558101	chr12:31876666-32006563	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	nsv1050448	chr12:31877289-31927006	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11051551	REP15	cis	parietal	SCAN
rs11051551	BICD1	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31882600-31886000	Weak transcription	Gastric	stomach
2	chr12:31882800-31886000	Weak transcription	Ovary	ovary
3	chr12:31882800-31887000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:31883000-31886000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:31883000-31886000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:31883000-31886000	Weak transcription	Pancreas	Pancrea
7	chr12:31883000-31886200	Weak transcription	Right Ventricle	heart
8	chr12:31883000-31887400	Enhancers	Placenta	Placenta
9	chr12:31883000-31896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:31883200-31886000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:31883200-31886000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:31883200-31886000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:31883200-31886000	Weak transcription	Brain Angular Gyrus	brain
14	chr12:31883200-31886000	Weak transcription	Lung	lung
15	chr12:31883200-31886000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:31883200-31886000	Enhancers	Hela-S3	cervix
17	chr12:31883200-31886200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:31883200-31886200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:31883200-31887000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:31883200-31887400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr12:31883200-31887600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:31883200-31887600	Enhancers	Fetal Thymus	thymus
23	chr12:31883200-31889400	Weak transcription	Primary T cells from cord blood	blood
24	chr12:31883400-31886600	Weak transcription	Thymus	Thymus
25	chr12:31883600-31886000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr12:31883800-31886000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:31883800-31886000	Weak transcription	Dnd41	blood
28	chr12:31883800-31886400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr12:31884000-31887400	Enhancers	Left Ventricle	heart
30	chr12:31884200-31886000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:31884200-31886200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:31884200-31886800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:31884200-31888800	Enhancers	NHDF-Ad	bronchial
34	chr12:31884400-31886000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:31884400-31887200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:31884400-31887400	Enhancers	Psoas Muscle	Psoas
37	chr12:31884600-31886000	Enhancers	NHEK	skin
38	chr12:31884600-31886200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:31884600-31886400	Enhancers	HepG2	liver
40	chr12:31884600-31886800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:31884600-31887200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr12:31884600-31887200	Enhancers	HSMM	muscle
43	chr12:31884600-31887400	Enhancers	Stomach Mucosa	stomach
44	chr12:31884600-31888000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:31884600-31889800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:31884800-31886000	Weak transcription	Aorta	Aorta
47	chr12:31884800-31886000	Weak transcription	Right Atrium	heart
48	chr12:31884800-31886400	Enhancers	Small Intestine	intestine
49	chr12:31884800-31886400	Enhancers	NHLF	lung
50	chr12:31884800-31887200	Enhancers	H1 Cell Line	embryonic stem cell

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