Variant report

Variant	rs73301996
Chromosome Location	chr17:19771804-19771805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr17:19771647-19771846	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr17:19770220-19771829	H1-hESC	embryonic stem cell:	n/a	n/a
3	SETDB1	chr17:19771252-19772230	U2OS	brain:	n/a	chr17:19772087-19772111
4	HA-E2F1	chr17:19770207-19772105	MCF-7	breast:	n/a	chr17:19771947-19771954 chr17:19770963-19770973 chr17:19771947-19771954 chr17:19771947-19771954 chr17:19770733-19770742
5	TCF12	chr17:19769721-19771998	A549	lung:	n/a	n/a
6	CTCF	chr17:19769654-19772275	A549	lung:	n/a	chr17:19771337-19771350 chr17:19771299-19771312 chr17:19770938-19770951 chr17:19771520-19771533 chr17:19771481-19771494
7	SIN3A	chr17:19770151-19772087	H1-hESC	embryonic stem cell:	n/a	chr17:19771287-19771296 chr17:19770959-19770970 chr17:19771169-19771180
8	KAP1	chr17:19770036-19771882	HEK293	kidney:	n/a	n/a
9	REST	chr17:19769877-19771959	H1-neurons	neurons:	n/a	chr17:19770786-19770800 chr17:19770788-19770798 chr17:19771004-19771017
10	POLR2A	chr17:19771792-19771983	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:19771783-19771833	SKMC	muscle:	n/a
2	chr17:19771783-19771833	BE2_C	brain:	n/a
3	chr17:19771783-19771833	AG04450	lung:	fetal
4	chr17:19771783-19771833	HIPEpiC	eye:	n/a
5	chr17:19771783-19771833	U87	brain:	n/a
6	chr17:19771783-19771833	SK-N-MC	brain:	n/a
7	chr17:19771783-19771833	AG09309	skin:	n/a
8	chr17:19771783-19771833	PFSK-1	brain:	n/a
9	chr17:19771783-19771833	K562	blood:	n/a
10	chr17:19771783-19771833	HMEC	breast:	n/a
11	chr17:19771783-19771833	AoSMC	blood vessel:	n/a
12	chr17:19771783-19771833	AG04449	skin:	fetal
13	chr17:19771783-19771833	HRPEpiC	eye:	n/a
14	chr17:19771783-19771833	ProgFib	skin:	n/a
15	chr17:19771783-19771833	HL-60	blood:	n/a
16	chr17:19771783-19771833	HCM	heart:	n/a
17	chr17:19771783-19771833	AG10803	skin:	n/a
18	chr17:19771783-19771833	AG09319	gingival:	n/a
19	chr17:19771783-19771833	SK-N-SH	brain:	n/a
20	chr17:19771783-19771833	HAEpiC	amniotic membrane:	n/a
21	chr17:19771783-19771833	NT2-D1	testis:	n/a
22	chr17:19771783-19771833	NH-A	brain:	n/a
23	chr17:19771783-19771833	RPTEC	kidney:	n/a
24	chr17:19771783-19771833	HRCEpiC	kidney:	n/a
25	chr17:19771783-19771833	Jurkat	blood:	n/a
26	chr17:19771783-19771833	T-47D	breast:	n/a
27	chr17:19771783-19771833	GM12878	blood:	n/a
28	chr17:19771783-19771833	LNCaP	prostate:	n/a
29	chr17:19771783-19771833	BJ	skin:	n/a
30	chr17:19771783-19771833	ECC-1	luminal epithelium:	n/a
31	chr17:19771783-19771833	MCF-7	breast:	n/a
32	chr17:19771783-19771833	H1-hESC	embryonic stem cell:	embryo
33	chr17:19771783-19771833	HPAEpiC	pulmonary alveolar:	n/a
34	chr17:19771783-19771833	ovcar-3	ovarian:	n/a
35	chr17:19771783-19771833	PrEC	prostate:	n/a
36	chr17:19771783-19771833	GM12891	blood:	n/a
37	chr17:19771783-19771833	HRE	kidney:	n/a
38	chr17:19771783-19771833	HCPEpiC	choroid plexus:	n/a
39	chr17:19771783-19771833	GM06990	blood:	n/a
40	chr17:19771783-19771833	Caco-2	colon:	n/a
41	chr17:19771783-19771833	HepG2	liver:	n/a
42	chr17:19771783-19771833	MCF10A-Er-Src	breast:	n/a
43	chr17:19771783-19771833	PANC-1	pancreas:	n/a
44	chr17:19771783-19771833	HCF	heart:	n/a
45	chr17:19771783-19771833	HCT-116	colon:	n/a
46	chr17:19771783-19771833	SAEC	small airway:	n/a
47	chr17:19771783-19771833	HNPCEpiC	eye:	n/a
48	chr17:19771783-19771833	GM12892	blood:	n/a
49	chr17:19771783-19771833	HEK293	kidney:	embryo
50	chr17:19771783-19771833	CMK	blood:	n/a

(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
ULK2	CpG island
ENSG00000083290	Chromatin interaction
ENSG00000108599	Chromatin interaction
ENSG00000270091	Chromatin interaction
ENSG00000261033	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs281325	0.88[AFR][1000 genomes]
rs281327	0.88[AFR][1000 genomes]
rs281338	0.88[AFR][1000 genomes]
rs281342	0.88[AFR][1000 genomes]
rs3101811	0.88[AFR][1000 genomes]
rs3101812	0.88[AFR][1000 genomes]
rs58920422	1.00[AFR][1000 genomes]
rs61381800	1.00[AFR][1000 genomes]
rs8066104	0.96[AFR][1000 genomes]

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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19769800-19772000	Active TSS	Brain Cingulate Gyrus	brain
2	chr17:19769800-19772000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr17:19769800-19772200	Active TSS	Fetal Kidney	kidney
4	chr17:19769800-19772200	Active TSS	Fetal Lung	lung
5	chr17:19770200-19772000	Active TSS	Fetal Intestine Small	intestine
6	chr17:19770400-19772200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:19770400-19772200	Active TSS	Stomach Smooth Muscle	stomach
8	chr17:19770400-19772200	Active TSS	Hela-S3	cervix
9	chr17:19770600-19772200	Active TSS	Liver	Liver
10	chr17:19771200-19772000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr17:19771200-19778800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:19771400-19772000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr17:19771400-19772000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr17:19771400-19772000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr17:19771400-19772000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr17:19771400-19772000	Enhancers	Fetal Brain Male	brain
17	chr17:19771400-19772200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:19771400-19772200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr17:19771600-19772000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr17:19771600-19772000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr17:19771600-19772000	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr17:19771600-19772000	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr17:19771600-19772000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr17:19771600-19772000	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr17:19771600-19772000	Flanking Active TSS	Fetal Brain Female	brain
26	chr17:19771600-19772200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr17:19771600-19772200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr17:19771600-19772200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr17:19771600-19772200	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr17:19771600-19772200	Bivalent Enhancer	Fetal Thymus	thymus
31	chr17:19771600-19772200	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr17:19771600-19774000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr17:19771600-19775000	Enhancers	Primary T cells fromperipheralblood	blood
34	chr17:19771600-19779000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr17:19771600-19787000	Weak transcription	Gastric	stomach
36	chr17:19771800-19772000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr17:19771800-19772000	Enhancers	Fetal Stomach	stomach
38	chr17:19771800-19772000	Active TSS	NH-A	brain
39	chr17:19771800-19772200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:19771800-19772200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
41	chr17:19771800-19772200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
42	chr17:19771800-19772200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr17:19771800-19772200	Enhancers	Esophagus	oesophagus
44	chr17:19771800-19772200	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr17:19771800-19772200	Bivalent Enhancer	Thymus	Thymus
46	chr17:19771800-19773200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr17:19771800-19775200	Enhancers	Primary T cells from cord blood	blood
48	chr17:19771800-19775200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr17:19771800-19776200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr17:19771800-19777800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links