Variant report

Variant	rs12910831
Chromosome Location	chr15:79043801-79043802
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	CTCF	chr15:79043290-79043827	MCF-7	breast:	n/a	chr15:79043461-79043474
2	HCFC1	chr15:79043059-79043907	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr15:79043402-79043894	GM19238	blood:	n/a	chr15:79043461-79043474
4	MAZ	chr15:79043243-79043804	IMR90	lung:	n/a	chr15:79043538-79043548
5	SMC3	chr15:79043190-79043962	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr15:79043395-79043861	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr15:79043261-79043899	HCT-116	colon:	n/a	n/a
8	CTCF	chr15:79043286-79043859	A549	lung:	n/a	chr15:79043461-79043474
9	RAD21	chr15:79043277-79043891	HCT-116	colon:	n/a	n/a
10	RAD21	chr15:79043294-79043813	ECC-1	luminal epithelium:	n/a	n/a
11	RAD21	chr15:79043291-79043807	MCF-7	breast:	n/a	n/a
12	CTCF	chr15:79043237-79043883	K562	blood:	n/a	chr15:79043461-79043474
13	CTCF	chr15:79043775-79043930	GM12891	blood:	n/a	n/a
14	RAD21	chr15:79043116-79044241	SK-N-SH	brain:	n/a	chr15:79044214-79044228 chr15:79044210-79044224
15	FOXM1	chr15:79043273-79043857	GM12878	blood:	n/a	n/a
16	CTCF	chr15:79043079-79043873	A549	lung:	n/a	chr15:79043461-79043474
17	CTCF	chr15:79043195-79043814	SK-N-SH	brain:	n/a	chr15:79043461-79043474
18	CTCF	chr15:79043394-79043933	Spleen_OC	spleen:	n/a	chr15:79043461-79043474

No.	Distal block	Cell Line	Cell type
1	chr15:78774775..78775285-chr15:79043113..79043866,2	MCF-7	breast:
2	chr15:78591118..78593802-chr15:79042531..79044066,2	K562	blood:
3	chr15:78292186..78292985-chr15:79043320..79043997,6	MCF-7	breast:
4	chr15:78292246..78292984-chr15:79043169..79044003,5	MCF-7	breast:
5	chr15:78291849..78292957-chr15:79043056..79044329,6	K562	blood:
6	chr15:78910576..78911172-chr15:79043464..79043998,2	MCF-7	breast:
7	chr15:78290955..78292806-chr15:79043518..79045037,2	MCF-7	breast:
8	chr15:78405703..78406239-chr15:79043526..79044041,2	K562	blood:
9	chr15:79006813..79007487-chr15:79043128..79043964,2	MCF-7	breast:
10	chr15:78910853..78911424-chr15:79043087..79043970,4	K562	blood:

Variant related genes	Relation type
ENSG00000238166	TF binding region
ENSG00000140395	Chromatin interaction
ENSG00000167202	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11072800	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632672	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11633152	0.85[AMR][1000 genomes]
rs12148817	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12904489	0.84[AMR][1000 genomes]
rs12906835	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12906977	0.84[AMR][1000 genomes]
rs12907207	0.84[AMR][1000 genomes]
rs12907432	0.84[AMR][1000 genomes]
rs12907536	0.84[AMR][1000 genomes]
rs12912245	0.89[AMR][1000 genomes]
rs12913779	0.84[AMR][1000 genomes]
rs12917502	0.92[AMR][1000 genomes]
rs2017091	0.84[AMR][1000 genomes]
rs2622821	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4887091	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4887092	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7182567	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7182694	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7182993	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs755998	0.84[AMR][1000 genomes]
rs8030090	0.85[AMR][1000 genomes]
rs8030335	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79033000-79045000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:79040600-79060000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:79042800-79044000	Enhancers	Brain Cingulate Gyrus	brain
4	chr15:79042800-79044000	Bivalent Enhancer	Fetal Stomach	stomach
5	chr15:79042800-79044000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr15:79042800-79045000	Enhancers	Fetal Heart	heart
7	chr15:79042800-79055400	Enhancers	Right Ventricle	heart
8	chr15:79043000-79044000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:79043000-79044000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr15:79043000-79044000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr15:79043000-79044000	Enhancers	Left Ventricle	heart
12	chr15:79043000-79044000	Enhancers	Stomach Mucosa	stomach
13	chr15:79043000-79044000	Enhancers	HUVEC	blood vessel
14	chr15:79043000-79044200	Enhancers	Primary B cells from peripheral blood	blood
15	chr15:79043000-79044200	Enhancers	Placenta	Placenta
16	chr15:79043000-79044400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr15:79043200-79044000	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr15:79043200-79044200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:79043200-79044200	Enhancers	Fetal Thymus	thymus
20	chr15:79043200-79044800	Weak transcription	Fetal Brain Male	brain
21	chr15:79043200-79047200	Weak transcription	NHDF-Ad	bronchial
22	chr15:79043400-79044000	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr15:79043400-79044000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr15:79043400-79044000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr15:79043400-79044000	Enhancers	Brain Hippocampus Middle	brain
26	chr15:79043400-79044000	Enhancers	Spleen	Spleen
27	chr15:79043400-79044200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr15:79043400-79044200	Enhancers	Stomach Smooth Muscle	stomach
29	chr15:79043400-79044600	Enhancers	Fetal Muscle Leg	muscle
30	chr15:79043400-79045400	Weak transcription	Right Atrium	heart
31	chr15:79043400-79046800	Enhancers	HSMMtube	muscle
32	chr15:79043400-79048200	Weak transcription	NH-A	brain
33	chr15:79043400-79048600	Weak transcription	Brain Angular Gyrus	brain
34	chr15:79043400-79049200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:79043400-79049200	Weak transcription	NHLF	lung
36	chr15:79043400-79049400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:79043400-79049600	Weak transcription	Pancreas	Pancrea
38	chr15:79043600-79044000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:79043600-79044000	Enhancers	Primary B cells from cord blood	blood
40	chr15:79043600-79044000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr15:79043600-79044000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr15:79043600-79044000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr15:79043600-79045600	Enhancers	HSMM	muscle
44	chr15:79043600-79046400	Weak transcription	A549	lung
45	chr15:79043600-79046800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:79043600-79046800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:79043600-79048200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:79043600-79048600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:79043600-79049600	Weak transcription	Colonic Mucosa	Colon
50	chr15:79043600-79049800	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links