Variant report

Variant	rs855141
Chromosome Location	chr12:47639821-47639822
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	EP300	chr12:47639233-47639972	A549	lung:	n/a	chr12:47639591-47639600
2	EP300	chr12:47639290-47639825	T-47D	breast:	n/a	chr12:47639591-47639600
3	ESR1	chr12:47639356-47639866	T-47D	breast:	n/a	n/a
4	GATA3	chr12:47639418-47639987	A549	lung:	n/a	n/a
5	EP300	chr12:47639209-47639972	T-47D	breast:	n/a	chr12:47639591-47639600
6	TEAD4	chr12:47639493-47639977	A549	lung:	n/a	n/a
7	TCF12	chr12:47639163-47640018	A549	lung:	n/a	chr12:47639645-47639654
8	FOXA1	chr12:47639298-47639936	T-47D	breast:	n/a	n/a
9	JUND	chr12:47639254-47639969	T-47D	breast:	n/a	chr12:47639591-47639601 chr12:47639592-47639600 chr12:47639593-47639600 chr12:47639592-47639600 chr12:47639590-47639602
10	JUND	chr12:47639192-47639916	T-47D	breast:	n/a	chr12:47639591-47639601 chr12:47639592-47639600 chr12:47639593-47639600 chr12:47639592-47639600 chr12:47639590-47639602
11	EP300	chr12:47639224-47639965	A549	lung:	n/a	chr12:47639591-47639600
12	GATA3	chr12:47639275-47639914	MCF-7	breast:	n/a	n/a
13	GATA3	chr12:47639255-47639966	MCF-7	breast:	n/a	n/a
14	BCL3	chr12:47639345-47639949	A549	lung:	n/a	n/a
15	CEBPB	chr12:47639442-47639916	A549	lung:	n/a	n/a
16	FOXA2	chr12:47639419-47640016	A549	lung:	n/a	n/a
17	TCF7L2	chr12:47639412-47639832	MCF-7	breast:	n/a	chr12:47639592-47639601
18	NR2F2	chr12:47639191-47639836	MCF-7	breast:	n/a	n/a
19	GATA3	chr12:47639232-47639918	T-47D	breast:	n/a	n/a
20	MAX	chr12:47639362-47639983	A549	lung:	n/a	chr12:47639591-47639600
21	SIN3AK20	chr12:47639291-47639917	MCF-7	breast:	n/a	n/a
22	FOXA2	chr12:47639380-47640040	A549	lung:	n/a	n/a
23	SP1	chr12:47639243-47639920	A549	lung:	n/a	n/a
24	SIN3AK20	chr12:47639267-47639927	MCF-7	breast:	n/a	n/a
25	RAD21	chr12:47639344-47639963	A549	lung:	n/a	n/a
26	FOSL2	chr12:47639513-47639862	A549	lung:	n/a	chr12:47639591-47639601 chr12:47639592-47639600 chr12:47639593-47639600 chr12:47639592-47639600 chr12:47639590-47639602
27	GATA3	chr12:47639302-47639829	T-47D	breast:	n/a	n/a
28	USF1	chr12:47639369-47639901	A549	lung:	n/a	n/a
29	REST	chr12:47639565-47639849	A549	lung:	n/a	n/a
30	GATA3	chr12:47639149-47639988	A549	lung:	n/a	n/a
31	ESR1	chr12:47639312-47639831	T-47D	breast:	n/a	n/a
32	SP1	chr12:47639235-47640048	A549	lung:	n/a	n/a
33	REST	chr12:47639272-47639946	A549	lung:	n/a	n/a
34	FOSL2	chr12:47639266-47639947	A549	lung:	n/a	chr12:47639591-47639601 chr12:47639592-47639600 chr12:47639593-47639600 chr12:47639592-47639600 chr12:47639590-47639602

No.	Distal block	Cell Line	Cell type
1	chr12:47616759..47619382-chr12:47639689..47641331,2	MCF-7	breast:
2	chr12:47474456..47476643-chr12:47638235..47640593,2	MCF-7	breast:
3	chr12:47638824..47640995-chr12:47669800..47672022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258181	TF binding region
ENSG00000179715	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs214660	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs214661	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835639	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs712100	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855143	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs855144	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855146	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855147	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855153	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855154	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47619000-47643600	Weak transcription	Pancreas	Pancrea
2	chr12:47629200-47643000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:47629400-47641200	Weak transcription	Aorta	Aorta
4	chr12:47630400-47644000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:47630400-47653600	Weak transcription	Primary B cells from cord blood	blood
6	chr12:47631600-47643000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:47632000-47643000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:47632600-47644600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:47632600-47646000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:47633200-47641200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:47633200-47653800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:47633400-47643200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:47636200-47653400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:47636400-47642600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:47636400-47643000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:47636600-47641200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:47636600-47641200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:47636600-47641200	Weak transcription	NHEK	skin
19	chr12:47636600-47642400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:47636600-47642400	Weak transcription	Primary T cells from cord blood	blood
21	chr12:47636600-47642400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:47636600-47642400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:47636600-47642600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:47636600-47643800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:47636600-47647000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:47639400-47643400	Weak transcription	Fetal Intestine Large	intestine
27	chr12:47639600-47642200	Weak transcription	K562	blood
28	chr12:47639800-47640400	Enhancers	A549	lung
29	chr12:47639800-47643800	Weak transcription	Spleen	Spleen

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