Variant report

Variant	rs11539482
Chromosome Location	chr3:141595160-141595161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:215)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:215 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:141594102-141597281	IMR90	lung:	n/a	n/a
2	CREB1	chr3:141594339-141595850	K562	blood:	n/a	n/a
3	YY1	chr3:141594967-141595966	GM12892	blood:	n/a	chr3:141595604-141595615 chr3:141595885-141595894 chr3:141595550-141595564 chr3:141595879-141595893 chr3:141595109-141595120 chr3:141595888-141595902 chr3:141595604-141595613 chr3:141595116-141595127 chr3:141595883-141595894 chr3:141595882-141595891
4	POLR2A	chr3:141595023-141595720	GM12878	blood:	n/a	n/a
5	TAF1	chr3:141594976-141595826	GM12878	blood:	n/a	n/a
6	MYC	chr3:141593847-141597213	A549	lung:	n/a	n/a
7	POLR2A	chr3:141595135-141595871	GM12878	blood:	n/a	n/a
8	MYC	chr3:141594339-141596459	K562	blood:	n/a	n/a
9	POLR2A	chr3:141594754-141595188	GM12891	blood:	n/a	n/a
10	POLR2A	chr3:141594849-141595867	GM10847	blood:	n/a	n/a
11	RCOR1	chr3:141595038-141595238	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:141594421-141596410	GM18951	blood:	n/a	n/a
13	CREB1	chr3:141594277-141595878	H1-hESC	embryonic stem cell:	n/a	n/a
14	CHD1	chr3:141594054-141598485	IMR90	lung:	n/a	chr3:141595830-141595840
15	NFIC	chr3:141594287-141595371	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:141594370-141596537	K562	blood:	n/a	n/a
17	POLR2A	chr3:141594326-141595884	HL-60	blood:	n/a	n/a
18	POLR2A	chr3:141594364-141595855	H1-neurons	neurons:	n/a	n/a
19	SPI1	chr3:141594889-141595184	GM12878	blood:	n/a	chr3:141595071-141595078
20	NR3C1	chr3:141594681-141595194	A549	lung:	n/a	n/a
21	FOXM1	chr3:141594290-141595359	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:141594253-141596909	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:141594366-141595168	PANC-1	pancreas:	n/a	n/a
24	CBX3	chr3:141594328-141595334	K562	blood:	n/a	n/a
25	UBTF	chr3:141594349-141596506	K562	blood:	n/a	n/a
26	MXI1	chr3:141594273-141595678	Hela-S3	cervix:	n/a	n/a
27	USF1	chr3:141594777-141595187	A549	lung:	n/a	chr3:141595111-141595127
28	TBP	chr3:141594377-141595798	K562	blood:	n/a	n/a
29	TCF7L2	chr3:141594260-141595265	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:141595035-141596152	HepG2	liver:	n/a	n/a
31	BHLHE40	chr3:141595074-141596555	GM12878	blood:	n/a	chr3:141595604-141595620 chr3:141595582-141595598 chr3:141595111-141595127 chr3:141595929-141595945
32	POLR2A	chr3:141594402-141596478	Raji	blood:	n/a	n/a
33	RUNX3	chr3:141594961-141595306	GM12878	blood:	n/a	n/a
34	MAX	chr3:141595080-141596512	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:141594700-141595228	GM12891	blood:	n/a	n/a
36	SMC3	chr3:141594152-141595264	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr3:141594447-141596456	MCF-7	breast:	n/a	n/a
38	POLR2A	chr3:141594443-141596424	GM18505	blood:	n/a	n/a
39	ZNF263	chr3:141594535-141595725	HEK293-T-REx	kidney:	n/a	n/a
40	POLR2A	chr3:141594412-141595899	K562	blood:	n/a	n/a
41	POLR2A	chr3:141594403-141595770	GM12891	blood:	n/a	n/a
42	POLR2A	chr3:141594342-141595389	PANC-1	pancreas:	n/a	n/a
43	SMARCB1	chr3:141594392-141596400	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:141594424-141595829	K562	blood:	n/a	n/a
45	TCF7L2	chr3:141594279-141596352	HCT-116	colon:	n/a	n/a
46	POLR2A	chr3:141594435-141596453	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:141594360-141596468	Hela-S3	cervix:	n/a	n/a
48	SIN3AK20	chr3:141594258-141595811	HCT-116	colon:	n/a	n/a
49	POLR2A	chr3:141594439-141596427	GM19193	blood:	n/a	n/a
50	BRCA1	chr3:141594098-141595233	Hela-S3	cervix:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141455674..141460093-chr3:141592801..141597430,19	MCF-7	breast:
2	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
3	chr16:31470762..31471597-chr3:141595023..141595997,2	Hela-S3	cervix:
4	chr3:141594674..141598943-chr3:141621711..141625603,5	MCF-7	breast:
5	chr3:141581516..141585437-chr3:141593335..141595315,3	K562	blood:
6	chr3:141592835..141597303-chr3:141629979..141635181,8	MCF-7	breast:
7	chr3:141456324..141457198-chr3:141594736..141595366,2	Hela-S3	cervix:
8	chr3:141456656..141457567-chr3:141593967..141595178,5	K562	blood:
9	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
10	chr3:141594460..141597483-chr3:141621419..141624479,3	K562	blood:
11	chr3:141582963..141586740-chr3:141593075..141596909,5	MCF-7	breast:
12	chr12:54674483..54675446-chr3:141595145..141596027,2	Hela-S3	cervix:
13	chr3:141296186..141298105-chr3:141594416..141596281,2	MCF-7	breast:
14	chr3:141296069..141298248-chr3:141594604..141596170,2	K562	blood:
15	chr17:29297677..29298316-chr3:141594597..141595457,2	Hela-S3	cervix:
16	chr1:26758364..26759241-chr3:141595118..141595810,2	HCT-116	colon:
17	chr3:141593925..141596999-chr3:141621116..141624479,3	K562	blood:
18	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:

No data

Variant related genes	Relation type
ATP1B3	TF binding region
ENSG00000181481	Chromatin interaction
ENSG00000114125	Chromatin interaction
ENSG00000069849	Chromatin interaction
ENSG00000155903	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000228398	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000117682	Chromatin interaction
ENSG00000200389	Chromatin interaction
ENSG00000260267	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3333253	chr3:141585303-141602936	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	esv3385430	chr3:141594412-141596710	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3325354	chr3:141594487-141597235	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
6	nsv591902	chr3:141594547-141596104	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141593400-141596600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:141593400-141597400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:141593400-141597600	Active TSS	Fetal Kidney	kidney
4	chr3:141593400-141597600	Active TSS	HMEC	breast
5	chr3:141593400-141597600	Active TSS	NHLF	lung
6	chr3:141593400-141598000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:141593600-141596400	Active TSS	Pancreas	Pancrea
8	chr3:141593600-141597000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:141593600-141597000	Active TSS	Placenta	Placenta
10	chr3:141593600-141597200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:141593600-141597600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:141593600-141598400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:141593800-141595600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:141593800-141596400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:141593800-141596600	Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:141593800-141596600	Active TSS	Brain Anterior Caudate	brain
17	chr3:141593800-141596800	Active TSS	Brain Hippocampus Middle	brain
18	chr3:141593800-141596800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr3:141593800-141596800	Active TSS	Fetal Brain Female	brain
20	chr3:141593800-141596800	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr3:141593800-141596800	Active TSS	Thymus	Thymus
22	chr3:141593800-141597200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:141593800-141597200	Active TSS	Brain Cingulate Gyrus	brain
24	chr3:141593800-141597200	Active TSS	NH-A	brain
25	chr3:141593800-141597200	Active TSS	NHDF-Ad	bronchial
26	chr3:141593800-141597400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr3:141593800-141597400	Active TSS	Stomach Smooth Muscle	stomach
28	chr3:141593800-141597400	Active TSS	HSMMtube	muscle
29	chr3:141593800-141597600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:141593800-141597600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr3:141593800-141597600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:141593800-141597600	Active TSS	Fetal Intestine Large	intestine
33	chr3:141593800-141597600	Active TSS	HSMM	muscle
34	chr3:141593800-141598000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:141593800-141598000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:141593800-141598000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:141593800-141598400	Active TSS	H1 Cell Line	embryonic stem cell
38	chr3:141594000-141595200	Active TSS	Fetal Brain Male	brain
39	chr3:141594000-141596000	Active TSS	Primary hematopoietic stem cells	blood
40	chr3:141594000-141596200	Active TSS	Rectal Smooth Muscle	rectum
41	chr3:141594000-141596600	Active TSS	Brain Substantia Nigra	brain
42	chr3:141594000-141596800	Active TSS	Brain Angular Gyrus	brain
43	chr3:141594000-141597600	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr3:141594000-141597600	Active TSS	Fetal Muscle Leg	muscle
45	chr3:141594000-141597600	Active TSS	Right Ventricle	heart
46	chr3:141594000-141598000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr3:141594200-141596800	Active TSS	Brain Germinal Matrix	brain
48	chr3:141594200-141597000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:141594200-141597600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:141594200-141598000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links