Variant report

Variant	rs6048540
Chromosome Location	chr20:23067809-23067810
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr20:23067712-23068113	GM12891	blood:	n/a	chr20:23067719-23067732
2	E2F6	chr20:23067687-23067832	K562	blood:	n/a	n/a
3	POLR2A	chr20:23065132-23067938	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr20:23063275-23068192	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr20:23067637-23067959	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr20:23067510-23067924	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr20:23067334-23068031	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr20:23061862-23067996	HUVEC	blood vessel:	n/a	n/a
9	MYC	chr20:23067593-23067874	HUVEC	blood vessel:	n/a	n/a
10	E2F6	chr20:23067528-23067977	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr20:23058358-23068293	HUVEC	blood vessel:	n/a	n/a
12	SPI1	chr20:23067779-23068094	GM12891	blood:	n/a	n/a
13	SPI1	chr20:23067708-23068075	GM12878	blood:	n/a	chr20:23067719-23067732
14	SPI1	chr20:23067551-23068987	GM12878	blood:	n/a	chr20:23067719-23067732

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:23067771-23067821	Caco-2	colon:	n/a
2	chr20:23067771-23067821	MCF-7	breast:	n/a
3	chr20:23067771-23067821	GM19239	blood:	n/a
4	chr20:23067771-23067821	K562	blood:	n/a
5	chr20:23067771-23067821	HRPEpiC	eye:	n/a
6	chr20:23067771-23067821	SK-N-MC	brain:	n/a
7	chr20:23067771-23067821	T-47D	breast:	n/a
8	chr20:23067771-23067821	SK-N-SH	brain:	n/a
9	chr20:23067771-23067821	HCF	heart:	n/a
10	chr20:23067771-23067821	ProgFib	skin:	n/a
11	chr20:23067771-23067821	HCPEpiC	choroid plexus:	n/a
12	chr20:23067771-23067821	NB4	blood:	n/a
13	chr20:23067771-23067821	HL-60	blood:	n/a
14	chr20:23067771-23067821	U87	brain:	n/a
15	chr20:23067771-23067821	GM12878	blood:	n/a
16	chr20:23067771-23067821	IMR90	lung:	fetal
17	chr20:23067771-23067821	HRCEpiC	kidney:	n/a
18	chr20:23067771-23067821	HAEpiC	amniotic membrane:	n/a
19	chr20:23067771-23067821	Jurkat	blood:	n/a
20	chr20:23067771-23067821	NHDF-neo	bronchial:	n/a
21	chr20:23067771-23067821	HPAEpiC	pulmonary alveolar:	n/a
22	chr20:23067771-23067821	PFSK-1	brain:	n/a
23	chr20:23067771-23067821	HCM	heart:	n/a
24	chr20:23067771-23067821	CMK	blood:	n/a
25	chr20:23067771-23067821	HUVEC	blood vessel:	n/a
26	chr20:23067771-23067821	LNCaP	prostate:	n/a
27	chr20:23067771-23067821	GM12892	blood:	n/a
28	chr20:23067771-23067821	H1-hESC	embryonic stem cell:	embryo
29	chr20:23067771-23067821	Hepatocyte	liver:	n/a
30	chr20:23067771-23067821	NHBE	bronchial:	n/a
31	chr20:23067771-23067821	HNPCEpiC	eye:	n/a
32	chr20:23067771-23067821	AG10803	skin:	n/a
33	chr20:23067771-23067821	HEK293	kidney:	embryo
34	chr20:23067771-23067821	GM06990	blood:	n/a
35	chr20:23067771-23067821	AG04450	lung:	fetal
36	chr20:23067771-23067821	RPTEC	kidney:	n/a
37	chr20:23067771-23067821	MCF10A-Er-Src	breast:	n/a
38	chr20:23067771-23067821	PANC-1	pancreas:	n/a
39	chr20:23067771-23067821	HEEpiC	esophagus:	n/a
40	chr20:23067771-23067821	SAEC	small airway:	n/a
41	chr20:23067771-23067821	AoSMC	blood vessel:	n/a
42	chr20:23067771-23067821	SKMC	muscle:	n/a
43	chr20:23067771-23067821	PrEC	prostate:	n/a
44	chr20:23067771-23067821	NT2-D1	testis:	n/a
45	chr20:23067771-23067821	AG04449	skin:	fetal
46	chr20:23067771-23067821	SK-N-SH_RA	brain:	n/a
47	chr20:23067771-23067821	AG09319	gingival:	n/a
48	chr20:23067771-23067821	ECC-1	luminal epithelium:	n/a
49	chr20:23067771-23067821	HIPEpiC	eye:	n/a
50	chr20:23067771-23067821	HRE	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23067329..23069872-chr20:23071485..23073602,2	MCF-7	breast:
2	chr20:23063365..23065588-chr20:23067624..23069134,2	K562	blood:

No data

Variant related genes	Relation type
CD93	TF binding region
CD93	CpG island

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv526474	chr20:23065209-23073904	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23064000-23072000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23064200-23072000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr20:23064200-23072400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr20:23064600-23068600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr20:23065800-23068400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr20:23066000-23075800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:23066600-23068000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:23066600-23068200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr20:23066600-23068200	Enhancers	Aorta	Aorta
10	chr20:23066600-23068200	Enhancers	K562	blood
11	chr20:23066600-23068800	Enhancers	GM12878-XiMat	blood
12	chr20:23066800-23068000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
13	chr20:23066800-23068000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr20:23066800-23068400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr20:23067000-23068200	Enhancers	Colon Smooth Muscle	Colon
16	chr20:23067000-23068400	Weak transcription	Right Ventricle	heart
17	chr20:23067000-23068600	Enhancers	Spleen	Spleen
18	chr20:23067000-23068800	Bivalent Enhancer	Fetal Stomach	stomach
19	chr20:23067000-23069000	Enhancers	Placenta	Placenta
20	chr20:23067000-23069200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr20:23067000-23072000	Weak transcription	Pancreas	Pancrea
22	chr20:23067000-23073800	Weak transcription	Esophagus	oesophagus
23	chr20:23067200-23068200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr20:23067200-23069000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr20:23067200-23069000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr20:23067200-23069200	Enhancers	Fetal Muscle Trunk	muscle
27	chr20:23067200-23071400	Weak transcription	Ovary	ovary
28	chr20:23067200-23072200	Weak transcription	Lung	lung
29	chr20:23067400-23068000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr20:23067400-23068000	Enhancers	Thymus	Thymus
31	chr20:23067400-23068600	Enhancers	HUVEC	blood vessel
32	chr20:23067400-23068800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr20:23067400-23069000	Enhancers	Fetal Thymus	thymus
34	chr20:23067400-23069400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr20:23067400-23069400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr20:23067400-23072400	Weak transcription	Fetal Lung	lung
37	chr20:23067600-23068000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr20:23067600-23068400	Enhancers	Right Atrium	heart
39	chr20:23067600-23068400	Enhancers	Stomach Smooth Muscle	stomach
40	chr20:23067600-23068600	Enhancers	Primary B cells from peripheral blood	blood
41	chr20:23067600-23068800	Enhancers	Adipose Nuclei	Adipose
42	chr20:23067600-23068800	Enhancers	Brain Substantia Nigra	brain
43	chr20:23067600-23069000	Enhancers	Fetal Muscle Leg	muscle
44	chr20:23067600-23069400	Enhancers	Primary hematopoietic stem cells	blood
45	chr20:23067800-23068000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr20:23067800-23068200	Enhancers	Primary B cells from cord blood	blood
47	chr20:23067800-23068400	Enhancers	Left Ventricle	heart
48	chr20:23067800-23069000	Enhancers	Primary T cells from cord blood	blood
49	chr20:23067800-23069400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr20:23067800-23069600	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links