Variant report

Variant	rs117397023
Chromosome Location	chr3:49054472-49054473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49052944-49056404	MCF10A-Er-Src	breast:	n/a	n/a
2	FOSL2	chr3:49054463-49055039	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:49050113-49067296	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:49053148-49056378	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:49052980-49056417	HL-60	blood:	n/a	n/a
6	POLR2A	chr3:49051503-49056616	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:49052474-49059791	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr3:49053662-49056450	U87	brain:	n/a	n/a
9	POLR2A	chr3:49049681-49055610	GM12891	blood:	n/a	n/a
10	PBX3	chr3:49053536-49056625	SK-N-SH	brain:	n/a	n/a
11	ZNF263	chr3:49054441-49055758	HEK293-T-REx	kidney:	n/a	n/a
12	SIN3AK20	chr3:49054346-49056362	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:49048502-49056486	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49048842-49056486	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:49053519-49054625	K562	blood:	n/a	n/a
16	POLR2A	chr3:49048845-49056419	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:49052548-49056350	K562	blood:	n/a	n/a
18	POLR2A	chr3:49051566-49056520	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:49053216-49054717	NB4	blood:	n/a	n/a
20	POLR2A	chr3:49051954-49056421	H1-hESC	embryonic stem cell:	n/a	n/a
21	BCL3	chr3:49053621-49054753	A549	lung:	n/a	n/a
22	POLR2A	chr3:49053617-49056538	U87	brain:	n/a	n/a
23	POLR2A	chr3:49051952-49055393	GM12892	blood:	n/a	n/a
24	POLR2A	chr3:49052566-49055998	A549	lung:	n/a	n/a
25	POLR2A	chr3:49053041-49054590	GM12891	blood:	n/a	n/a
26	POLR2A	chr3:49050908-49056374	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr3:49052097-49056367	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr3:49052736-49056323	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:49048918-49055399	GM12892	blood:	n/a	n/a
30	POLR2A	chr3:49053331-49056321	HUVEC	blood vessel:	n/a	n/a
31	POU2F2	chr3:49053810-49054594	GM12891	blood:	n/a	n/a
32	POLR2A	chr3:49053819-49054764	GM19193	blood:	n/a	n/a
33	POLR2A	chr3:49053369-49054579	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:49048783-49056505	GM12892	blood:	n/a	n/a
35	POLR2A	chr3:49054163-49056367	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr3:49052798-49054881	SK-N-SH	brain:	n/a	n/a
37	MTA3	chr3:49053209-49056613	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:49048897-49056290	GM12891	blood:	n/a	n/a
39	POLR2A	chr3:49051541-49056898	K562	blood:	n/a	n/a
40	POLR2A	chr3:49053209-49056861	GM12891	blood:	n/a	n/a
41	MXI1	chr3:49054354-49056631	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:49052889-49056613	HCT-116	colon:	n/a	n/a
43	POU2F2	chr3:49053765-49054803	GM12891	blood:	n/a	n/a
44	POLR2A	chr3:49052846-49056620	K562	blood:	n/a	n/a
45	POLR2A	chr3:49053880-49054871	Hela-S3	cervix:	n/a	n/a
46	PML	chr3:49052717-49056611	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:49052988-49056596	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr3:49053373-49056652	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr3:49054279-49054575	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:49052283-49056597	HL-60	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49054288..49061452-chr3:49128946..49133927,24	K562	blood:
2	chr3:49052737..49055601-chr3:49169653..49171785,2	MCF-7	breast:
3	chr14:105265057..105267677-chr3:49054198..49056753,2	MCF-7	breast:
4	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
5	chr3:49050440..49054790-chr3:49130798..49133846,4	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFAF3	TF binding region
DALRD3	TF binding region
ENSG00000172037	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000179627	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	esv3323398	chr3:49053998-49056796	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49045800-49055000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49046200-49054600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:49046200-49054600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:49046200-49054800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:49047600-49054800	Strong transcription	Lung	lung
6	chr3:49048400-49054600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49048800-49054600	Strong transcription	Fetal Brain Female	brain
8	chr3:49048800-49054600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr3:49048800-49054800	Strong transcription	Brain Cingulate Gyrus	brain
10	chr3:49049000-49054600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49049000-49054600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:49049000-49054600	Strong transcription	Brain Anterior Caudate	brain
13	chr3:49049000-49054600	Strong transcription	Brain Hippocampus Middle	brain
14	chr3:49049000-49054600	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr3:49049000-49054600	Strong transcription	Rectal Smooth Muscle	rectum
16	chr3:49049000-49054600	Strong transcription	Osteobl	bone
17	chr3:49049200-49054800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:49049200-49054800	Strong transcription	Fetal Lung	lung
19	chr3:49050400-49054800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:49050800-49054600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:49051200-49054600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:49051200-49054600	Strong transcription	Right Ventricle	heart
23	chr3:49051200-49054800	Weak transcription	Psoas Muscle	Psoas
24	chr3:49051400-49055000	Weak transcription	Right Atrium	heart
25	chr3:49051600-49054600	Strong transcription	Placenta	Placenta
26	chr3:49051600-49054600	Strong transcription	HSMM	muscle
27	chr3:49051800-49054600	Weak transcription	Fetal Heart	heart
28	chr3:49052600-49054600	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:49052600-49054800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:49053000-49054800	Weak transcription	Small Intestine	intestine
31	chr3:49053000-49054800	Weak transcription	HUVEC	blood vessel
32	chr3:49053400-49054600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:49053400-49056000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:49053600-49054800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:49053600-49054800	Genic enhancers	Pancreas	Pancrea
36	chr3:49053800-49054600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:49053800-49054600	Weak transcription	Fetal Brain Male	brain
38	chr3:49053800-49054600	Genic enhancers	Fetal Thymus	thymus
39	chr3:49053800-49054800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:49053800-49054800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:49053800-49054800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:49053800-49054800	Weak transcription	Fetal Kidney	kidney
43	chr3:49053800-49054800	Weak transcription	Ovary	ovary
44	chr3:49053800-49055000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:49053800-49055000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:49053800-49055000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:49053800-49055200	Weak transcription	Aorta	Aorta
48	chr3:49054000-49054600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:49054000-49054600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:49054000-49054600	Weak transcription	Monocytes-CD14+_RO01746	blood

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