Variant report

Variant	rs12944699
Chromosome Location	chr17:46049378-46049379
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr17:46047522-46050410	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr17:46047255-46050557	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr17:46047494-46049540	IMR90	lung:	n/a	n/a
4	NR2F2	chr17:46047840-46049590	K562	blood:	n/a	n/a
5	CTCF	chr17:46047393-46050115	A549	lung:	n/a	chr17:46048168-46048177
6	GTF3C2	chr17:46048864-46049401	Hela-S3	cervix:	n/a	n/a
7	RPC155	chr17:46048911-46049505	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:46047811-46049607	HepG2	liver:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45916805..45918645-chr17:46049307..46052220,2	MCF-7	breast:
2	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
3	chr17:45932084..45934510-chr17:46047359..46049635,2	K562	blood:
4	chr17:45915738..45918906-chr17:46047433..46049662,3	K562	blood:
5	chr17:46048621..46050545-chr17:46057076..46059668,3	K562	blood:
6	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
7	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
8	chr17:45971266..45974117-chr17:46049059..46051074,2	MCF-7	breast:
9	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
10	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
11	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
12	chr17:45727256..45728937-chr17:46047807..46049675,2	K562	blood:
13	chr17:46048432..46050374-chr17:46050535..46053358,3	MCF-7	breast:
14	chr17:46048551..46050173-chr17:46123931..46126830,2	MCF-7	breast:
15	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
16	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:
17	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
18	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
19	chr17:46048370..46050701-chr17:46124898..46126529,2	K562	blood:
20	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
21	chr17:46048142..46050112-chr17:46183426..46185210,2	K562	blood:

No data

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12941306	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12942412	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12945188	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12945362	1.00[AMR][1000 genomes]
rs12945768	1.00[AMR][1000 genomes]
rs12947761	1.00[AMR][1000 genomes]
rs12947966	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12948207	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16952687	1.00[AMR][1000 genomes]
rs34033530	1.00[AMR][1000 genomes]
rs34038169	1.00[AMR][1000 genomes]
rs34153693	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34166016	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34358803	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34601263	0.94[AFR][1000 genomes]
rs34632031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34822864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34958507	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35177469	1.00[AMR][1000 genomes]
rs35273388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35350665	1.00[AMR][1000 genomes]
rs35534834	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35551276	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35647888	1.00[AMR][1000 genomes]
rs35677091	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35711165	1.00[AMR][1000 genomes]
rs35751035	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35766594	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35778085	1.00[AMR][1000 genomes]
rs35795560	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35848720	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35928933	1.00[AMR][1000 genomes]
rs36059789	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36090279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56078988	1.00[AMR][1000 genomes]
rs56363348	1.00[AMR][1000 genomes]
rs57864674	1.00[AMR][1000 genomes]
rs57948485	1.00[AMR][1000 genomes]
rs58974249	1.00[AMR][1000 genomes]
rs59483607	1.00[AMR][1000 genomes]
rs59727791	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60224300	1.00[AMR][1000 genomes]
rs60525548	1.00[AMR][1000 genomes]
rs6503951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71369826	0.83[AFR][1000 genomes]
rs71377331	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377332	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377338	1.00[AMR][1000 genomes]
rs71377341	1.00[AMR][1000 genomes]
rs71377342	1.00[AMR][1000 genomes]
rs73985416	1.00[AMR][1000 genomes]
rs73985417	1.00[AMR][1000 genomes]
rs73985418	1.00[AMR][1000 genomes]
rs73985419	1.00[AMR][1000 genomes]
rs73985421	1.00[AMR][1000 genomes]
rs73985422	1.00[AMR][1000 genomes]
rs73985424	1.00[AMR][1000 genomes]
rs73985479	1.00[AMR][1000 genomes]
rs8075711	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 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	chr17:46047000-46049400	Active TSS	Rectal Smooth Muscle	rectum
2	chr17:46047600-46049400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:46047600-46049600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:46047800-46049400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr17:46047800-46049400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr17:46047800-46050000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr17:46048000-46049400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr17:46048000-46049400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:46048000-46049400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr17:46048000-46049400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr17:46048000-46049400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:46048000-46049400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:46048000-46049400	Active TSS	Colonic Mucosa	Colon
14	chr17:46048000-46049400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr17:46048000-46049400	Active TSS	Ovary	ovary
16	chr17:46048000-46049400	Active TSS	GM12878-XiMat	blood
17	chr17:46048000-46049400	Active TSS	HSMM	muscle
18	chr17:46048000-46049400	Active TSS	NHDF-Ad	bronchial
19	chr17:46048000-46049600	Active TSS	HSMMtube	muscle
20	chr17:46048000-46049800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr17:46048400-46049400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:46048600-46049400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:46048600-46049400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr17:46048600-46049400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr17:46048600-46049400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr17:46048600-46049400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr17:46048600-46049400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr17:46048600-46049400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr17:46048600-46049400	Flanking Active TSS	Fetal Thymus	thymus
30	chr17:46048600-46049400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr17:46048600-46049400	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr17:46048600-46049600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr17:46048600-46049800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:46048600-46049800	Flanking Active TSS	Liver	Liver
35	chr17:46048600-46049800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr17:46048600-46050000	Flanking Active TSS	Dnd41	blood
37	chr17:46048800-46049400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr17:46048800-46049400	Flanking Active TSS	Fetal Lung	lung
39	chr17:46048800-46049400	Flanking Active TSS	Fetal Stomach	stomach
40	chr17:46048800-46049600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr17:46048800-46049600	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr17:46048800-46049600	Flanking Active TSS	HepG2	liver
43	chr17:46048800-46050000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr17:46049000-46049400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:46049000-46049400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr17:46049000-46049400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr17:46049000-46049400	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr17:46049000-46049400	Flanking Active TSS	Right Ventricle	heart
49	chr17:46049000-46049400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr17:46049000-46049600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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