Variant report

Variant	rs576004028
Chromosome Location	chr17:19770508-19770509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:228)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:228 , 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	TBP	chr17:19770294-19771579	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr17:19770047-19771566	A549	lung:	n/a	n/a
3	CTCF	chr17:19770360-19770510	HVMF	connective:	n/a	n/a
4	YY1	chr17:19770366-19770671	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:19770239-19771509	A549	lung:	n/a	n/a
6	CTCF	chr17:19770336-19770542	LNCaP	prostate:	n/a	n/a
7	POLR2A	chr17:19770334-19771429	IMR90	lung:	n/a	n/a
8	CTCF	chr17:19770371-19770560	ProgFib	skin:	n/a	n/a
9	CTCF	chr17:19770460-19770610	GM12869	blood:	n/a	n/a
10	POLR2A	chr17:19770261-19771438	GM18951	blood:	n/a	n/a
11	MAX	chr17:19770097-19771550	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr17:19770288-19770741	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr17:19770380-19770530	HEK293	kidney:	n/a	n/a
14	POLR2A	chr17:19770307-19771374	GM12878	blood:	n/a	n/a
15	EBF1	chr17:19770215-19770559	GM12878	blood:	n/a	n/a
16	JUND	chr17:19770067-19771550	A549	lung:	n/a	chr17:19770760-19770769
17	CTCF	chr17:19770357-19770517	GM12878	blood:	n/a	n/a
18	CTCF	chr17:19770252-19770600	IMR90	lung:	n/a	n/a
19	MYC	chr17:19770421-19770514	HUVEC	blood vessel:	n/a	n/a
20	CTCF	chr17:19770325-19770530	NHEK	skin:	n/a	n/a
21	CTBP2	chr17:19770220-19771829	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAZ	chr17:19769994-19770556	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr17:19770126-19771589	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr17:19770436-19770666	GM12892	blood:	n/a	n/a
25	MAX	chr17:19770149-19770992	HepG2	liver:	n/a	n/a
26	POLR2A	chr17:19770165-19770640	PFSK-1	brain:	n/a	n/a
27	CTCF	chr17:19770380-19770530	Caco-2	colon:	n/a	n/a
28	CTCF	chr17:19770360-19770510	SK-N-SH_RA	brain:	n/a	n/a
29	POLR2A	chr17:19770242-19770676	HUVEC	blood vessel:	n/a	n/a
30	CTCF	chr17:19770325-19770592	GM12878	blood:	n/a	n/a
31	CTCF	chr17:19770400-19770550	HPAF	blood vessel:	n/a	n/a
32	CTCF	chr17:19770360-19770510	MCF-7	breast:	n/a	n/a
33	CTCF	chr17:19770360-19770510	HRE	kidney:	n/a	n/a
34	TFAP2C	chr17:19769847-19770669	Hela-S3	cervix:	n/a	chr17:19770199-19770214
35	POLR2A	chr17:19770123-19770704	SK-N-SH	brain:	n/a	n/a
36	CTCF	chr17:19770380-19770530	GM12864	blood:	n/a	n/a
37	POLR2A	chr17:19769869-19771551	MCF10A-Er-Src	breast:	n/a	n/a
38	CTCF	chr17:19770380-19770530	AG04450	lung:	n/a	n/a
39	RAD21	chr17:19770321-19770553	HepG2	liver:	n/a	n/a
40	POLR2A	chr17:19770301-19770547	GM12892	blood:	n/a	n/a
41	CTCF	chr17:19770360-19770510	AG10803	skin:	n/a	n/a
42	RAD21	chr17:19770286-19770567	SK-N-SH_RA	brain:	n/a	n/a
43	ELF1	chr17:19770068-19771543	GM12878	blood:	n/a	chr17:19770936-19770948 chr17:19770968-19770980 chr17:19771201-19771210 chr17:19771397-19771409 chr17:19771003-19771012
44	POLR2A	chr17:19770225-19771410	HCT-116	colon:	n/a	n/a
45	ELK1	chr17:19770322-19770509	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr17:19770420-19771388	GM10847	blood:	n/a	n/a
47	MAX	chr17:19770181-19771535	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr17:19770369-19770526	Pancreas_OC	pancreas:	n/a	n/a
49	CTCF	chr17:19770360-19770510	RPTEC	kidney:	n/a	n/a
50	CTCF	chr17:19770460-19770610	GM12873	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:19769588..19772074-chr17:19879592..19882526,4	MCF-7	breast:
2	chr17:19769802..19772027-chr17:19799780..19804333,4	MCF-7	breast:
3	chr17:19752348..19754374-chr17:19768940..19771870,2	MCF-7	breast:
4	chr17:19769754..19773058-chr17:19878983..19882883,4	MCF-7	breast:
5	chr17:19770311..19771954-chr17:19910328..19912594,2	MCF-7	breast:

No data

Variant related genes	Relation type
ULK2	TF binding region
ENSG00000270091	Chromatin interaction
ENSG00000261033	Chromatin interaction
ENSG00000083290	Chromatin interaction
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1057469	chr17:19696714-19787062	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3371214	chr17:19768660-19773258	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv3402031	chr17:19769585-19772133	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19768600-19771400	Active TSS	GM12878-XiMat	blood
2	chr17:19769000-19771800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr17:19769200-19771400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr17:19769400-19771400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:19769400-19771400	Active TSS	Brain Anterior Caudate	brain
6	chr17:19769400-19771800	Active TSS	A549	lung
7	chr17:19769600-19771800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr17:19769800-19770600	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr17:19769800-19770600	Active TSS	Fetal Brain Male	brain
10	chr17:19769800-19770600	Active TSS	Fetal Heart	heart
11	chr17:19769800-19770600	Flanking Active TSS	Placenta	Placenta
12	chr17:19769800-19770800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:19769800-19770800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr17:19769800-19770800	Flanking Active TSS	HMEC	breast
15	chr17:19769800-19771000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr17:19769800-19771400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr17:19769800-19771400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr17:19769800-19771400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr17:19769800-19771400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr17:19769800-19771600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr17:19769800-19771600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr17:19769800-19771600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:19769800-19771600	Active TSS	Muscle Satellite Cultured Cells	--
24	chr17:19769800-19771600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr17:19769800-19771600	Active TSS	Fetal Intestine Large	intestine
26	chr17:19769800-19771600	Active TSS	Fetal Stomach	stomach
27	chr17:19769800-19771800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr17:19769800-19771800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:19769800-19771800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr17:19769800-19771800	Active TSS	Ovary	ovary
31	chr17:19769800-19771800	Active TSS	Psoas Muscle	Psoas
32	chr17:19769800-19771800	Active TSS	Right Atrium	heart
33	chr17:19769800-19771800	Active TSS	HSMM	muscle
34	chr17:19769800-19771800	Active TSS	NHDF-Ad	bronchial
35	chr17:19769800-19772000	Active TSS	Brain Cingulate Gyrus	brain
36	chr17:19769800-19772000	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr17:19769800-19772200	Active TSS	Fetal Kidney	kidney
38	chr17:19769800-19772200	Active TSS	Fetal Lung	lung
39	chr17:19770000-19770600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr17:19770000-19770600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr17:19770000-19770600	Flanking Active TSS	Liver	Liver
42	chr17:19770000-19770600	Flanking Active TSS	Colonic Mucosa	Colon
43	chr17:19770000-19771000	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr17:19770000-19771000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:19770000-19771200	Bivalent/Poised TSS	Thymus	Thymus
46	chr17:19770000-19771400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr17:19770000-19771400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:19770000-19771400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr17:19770000-19771400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr17:19770000-19771400	Active TSS	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links