Variant report

Variant	rs73981808
Chromosome Location	chr17:19998489-19998490
allele	C/T
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	MAX	chr17:19998482-19999121	A549	lung:	n/a	n/a
2	RAD21	chr17:19998444-19999234	A549	lung:	n/a	chr17:19998781-19998795 chr17:19998728-19998740
3	RAD21	chr17:19998159-19999582	SK-N-SH	brain:	n/a	chr17:19998781-19998795 chr17:19998728-19998740
4	KAP1	chr17:19998316-19999070	HEK293	kidney:	n/a	n/a
5	RAD21	chr17:19998483-19999032	A549	lung:	n/a	chr17:19998781-19998795 chr17:19998728-19998740
6	CTCF	chr17:19998423-19999522	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr17:19998486-19998986	MCF-7	breast:	n/a	chr17:19998781-19998795 chr17:19998728-19998740
8	KAP1	chr17:19998430-19999216	U2OS	brain:	n/a	n/a
9	MXI1	chr17:19998190-19999434	SK-N-SH	brain:	n/a	chr17:19998462-19998477
10	CTCF	chr17:19998181-19999885	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19912080..19913024-chr17:19997997..19998740,2	K562	blood:
2	chr17:19912162..19913083-chr17:19998469..19999472,3	MCF-7	breast:

Variant related genes	Relation type
SPECC1	TF binding region
ENSG00000261033	Chromatin interaction
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs57127528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
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]
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:9 , 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	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

No data

Chromatin state (count:67 , 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	chr17:19990200-19998800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19993600-19998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:19993600-20000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:19993600-20003600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:19993800-19998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:19993800-19998800	Weak transcription	Spleen	Spleen
9	chr17:19993800-20000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:19993800-20001600	Weak transcription	Lung	lung
11	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
12	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
13	chr17:19994600-19998600	Enhancers	Brain Hippocampus Middle	brain
14	chr17:19995000-20000000	Weak transcription	Right Ventricle	heart
15	chr17:19995000-20001200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr17:19995200-19998800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:19995400-19998600	Enhancers	Adipose Nuclei	Adipose
18	chr17:19995800-19998800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr17:19996600-20000800	Weak transcription	Aorta	Aorta
20	chr17:19996800-19998800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr17:19996800-19998800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:19996800-19998800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:19996800-19999600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr17:19997000-19998600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:19997000-19998800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr17:19997000-19998800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:19997000-19998800	Weak transcription	Left Ventricle	heart
28	chr17:19997400-19998600	Weak transcription	Right Atrium	heart
29	chr17:19997600-19998800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:19997600-19998800	Weak transcription	Ovary	ovary
31	chr17:19997600-19999600	Enhancers	Fetal Muscle Leg	muscle
32	chr17:19997800-19999000	Enhancers	NHLF	lung
33	chr17:19997800-19999200	Enhancers	Brain Germinal Matrix	brain
34	chr17:19997800-19999200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr17:19998200-19998600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:19998200-19998600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr17:19998200-19998600	Enhancers	NHDF-Ad	bronchial
38	chr17:19998200-19998600	Enhancers	Osteobl	bone
39	chr17:19998200-19999000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr17:19998200-19999000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr17:19998200-19999200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:19998200-19999200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:19998200-19999200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr17:19998200-20000000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr17:19998200-20000000	Enhancers	Brain Substantia Nigra	brain
46	chr17:19998400-19998600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr17:19998400-19998600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:19998400-19998600	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr17:19998400-19998600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:19998400-19998600	Flanking Active TSS	HMEC	breast

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