Variant report

Variant	rs57127528
Chromosome Location	chr17:19989985-19989986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:19989780-19990017	MCF-7	breast:	n/a	chr17:19989803-19989812
2	RAD21	chr17:19989693-19990121	MCF-7	breast:	n/a	n/a
3	GATA3	chr17:19989645-19990221	MCF-7	breast:	n/a	chr17:19989937-19989945
4	GATA3	chr17:19989784-19990094	SH-SY5Y	brain:	n/a	chr17:19989937-19989945
5	CTCF	chr17:19989678-19989985	K562	blood:	n/a	chr17:19989803-19989812
6	JUND	chr17:19989692-19990074	K562	blood:	n/a	n/a
7	MYC	chr17:19989762-19990013	MCF-7	breast:	n/a	chr17:19989981-19989991
8	GATA3	chr17:19989566-19990362	MCF-7	breast:	n/a	chr17:19989937-19989945
9	CTCF	chr17:19989563-19990029	MCF-7	breast:	n/a	chr17:19989803-19989812
10	RCOR1	chr17:19989854-19990020	K562	blood:	n/a	n/a
11	MAX	chr17:19989676-19990022	K562	blood:	n/a	chr17:19989981-19989991
12	CTCF	chr17:19989719-19990095	K562	blood:	n/a	chr17:19989803-19989812
13	GATA3	chr17:19989761-19990089	MCF-7	breast:	n/a	chr17:19989937-19989945
14	GATA2	chr17:19989729-19990148	SH-SY5Y	brain:	n/a	n/a
15	MAX	chr17:19989675-19990088	MCF-7	breast:	n/a	chr17:19989981-19989991
16	GATA3	chr17:19989756-19990096	T-47D	breast:	n/a	chr17:19989937-19989945

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19880813..19883681-chr17:19988880..19990706,2	MCF-7	breast:

Variant related genes	Relation type
SPECC1	TF binding region
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs58334454	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58338147	1.00[AMR][1000 genomes]
rs58748150	1.00[AMR][1000 genomes]
rs60321315	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60740483	1.00[AMR][1000 genomes]
rs7215558	1.00[AMR][1000 genomes]
rs7225930	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980789	1.00[AMR][1000 genomes]
rs73980790	1.00[AMR][1000 genomes]
rs73980791	1.00[AMR][1000 genomes]
rs73980793	1.00[AMR][1000 genomes]
rs73980794	1.00[AMR][1000 genomes]
rs73980795	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980797	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73981806	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73981808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73981810	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73984562	1.00[AMR][1000 genomes]
rs73984563	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8066256	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv2762522	chr17:19976462-19996429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:19980600-19994600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:19980800-19990000	Weak transcription	A549	lung
4	chr17:19981200-19993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:19982600-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:19983200-19993400	Weak transcription	Spleen	Spleen
7	chr17:19985600-19993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:19986200-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr17:19986400-19990600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:19986400-19991400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:19987000-19994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:19987800-19990200	Enhancers	NHDF-Ad	bronchial
13	chr17:19988000-19990200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:19988000-19990200	Enhancers	Ovary	ovary
15	chr17:19988000-19991200	Enhancers	Brain Angular Gyrus	brain
16	chr17:19988200-19990000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr17:19988200-19990200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:19988200-19990200	Enhancers	Brain Anterior Caudate	brain
19	chr17:19988200-19990200	Enhancers	Brain Hippocampus Middle	brain
20	chr17:19988200-19990200	Enhancers	Brain Substantia Nigra	brain
21	chr17:19988200-19990200	Enhancers	Left Ventricle	heart
22	chr17:19988200-19990200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr17:19988200-19990200	Enhancers	NH-A	brain
24	chr17:19988200-19990400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:19988200-19990400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr17:19988200-19990400	Enhancers	Fetal Muscle Trunk	muscle
27	chr17:19988200-19990600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:19988200-19991000	Enhancers	HSMMtube	muscle
29	chr17:19988200-19991200	Enhancers	Adipose Nuclei	Adipose
30	chr17:19988200-19991200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:19988400-19990200	Enhancers	Esophagus	oesophagus
32	chr17:19988400-19990400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr17:19988600-19990000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:19988600-19990200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr17:19988600-19993200	Weak transcription	GM12878-XiMat	blood
36	chr17:19988600-19994600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr17:19988800-19991400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:19988800-19994600	Weak transcription	Right Atrium	heart
39	chr17:19989000-19990400	Enhancers	Brain Cingulate Gyrus	brain
40	chr17:19989000-19994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr17:19989200-19990200	Enhancers	Aorta	Aorta
42	chr17:19989200-19991600	Enhancers	Fetal Muscle Leg	muscle
43	chr17:19989200-19994200	Weak transcription	Osteobl	bone
44	chr17:19989400-19990200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:19989400-19990200	Enhancers	Right Ventricle	heart
46	chr17:19989400-19994200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:19989600-19990000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr17:19989600-19990200	Enhancers	K562	blood
49	chr17:19989600-19991200	Enhancers	Stomach Mucosa	stomach
50	chr17:19989600-19994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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