Variant report

Variant	rs12941306
Chromosome Location	chr17:46047329-46047330
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr17:46047255-46050557	SK-N-SH	brain:	n/a	n/a
2	SIN3AK20	chr17:46047317-46049226	MCF-7	breast:	n/a	n/a
3	RCOR1	chr17:46047323-46047604	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46046297..46048098-chr17:46050701..46053030,2	MCF-7	breast:
2	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
3	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
4	chr17:45917404..45919085-chr17:46045221..46048078,2	K562	blood:
5	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
6	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
7	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
8	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
9	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
10	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
11	chr17:46046859..46048450-chr17:46055513..46058232,2	K562	blood:

No data

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000167183	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000234494	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12939977	0.81[AFR][1000 genomes]
rs12942412	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12944699	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12945188	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12945362	1.00[AMR][1000 genomes]
rs12945768	1.00[AMR][1000 genomes]
rs12947761	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12947966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12948207	1.00[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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34166016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34358803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34601263	1.00[AFR][1000 genomes]
rs34632031	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34822864	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34958507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35177469	1.00[AMR][1000 genomes]
rs35273388	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35350665	1.00[AMR][1000 genomes]
rs35534834	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35551276	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35647888	1.00[AMR][1000 genomes]
rs35677091	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35711165	1.00[AMR][1000 genomes]
rs35751035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35766594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35778085	1.00[AMR][1000 genomes]
rs35795560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35848720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35928933	1.00[AMR][1000 genomes]
rs36059789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36090279	0.94[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60224300	1.00[AMR][1000 genomes]
rs60525548	1.00[AMR][1000 genomes]
rs6503951	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71369826	0.88[AFR][1000 genomes]
rs71377331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377334	0.94[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	0.90[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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
2	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
3	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:46035000-46047400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr17:46036600-46047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:46036800-46047400	Weak transcription	Thymus	Thymus
9	chr17:46037800-46047400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:46037800-46047400	Enhancers	Fetal Intestine Small	intestine
11	chr17:46037800-46047800	Enhancers	Fetal Intestine Large	intestine
12	chr17:46039600-46047600	Weak transcription	Primary T cells from cord blood	blood
13	chr17:46042800-46047800	Weak transcription	Small Intestine	intestine
14	chr17:46043000-46047800	Enhancers	Pancreas	Pancrea
15	chr17:46043000-46047800	Enhancers	Stomach Mucosa	stomach
16	chr17:46044200-46047600	Weak transcription	Liver	Liver
17	chr17:46044800-46048000	Enhancers	Placenta	Placenta
18	chr17:46045000-46047800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr17:46045200-46047600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr17:46045200-46047600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr17:46045400-46047400	Weak transcription	Colon Smooth Muscle	Colon
22	chr17:46045400-46047600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr17:46045400-46047600	Weak transcription	HSMM	muscle
24	chr17:46045400-46047800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr17:46045400-46047800	Weak transcription	Lung	lung
26	chr17:46045400-46048400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr17:46045600-46047400	Weak transcription	HepG2	liver
28	chr17:46045600-46047600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:46045600-46047600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:46045600-46047600	Weak transcription	Osteobl	bone
31	chr17:46045600-46047800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:46045800-46047400	Weak transcription	HMEC	breast
33	chr17:46045800-46047600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr17:46045800-46047600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:46045800-46047600	Weak transcription	NHEK	skin
36	chr17:46045800-46047800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:46045800-46047800	Weak transcription	Ovary	ovary
38	chr17:46045800-46047800	Weak transcription	HSMMtube	muscle
39	chr17:46045800-46047800	Weak transcription	NH-A	brain
40	chr17:46045800-46047800	Weak transcription	NHDF-Ad	bronchial
41	chr17:46045800-46047800	Weak transcription	NHLF	lung
42	chr17:46046000-46047400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:46046000-46047600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr17:46046400-46047600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:46046600-46047400	Weak transcription	A549	lung
46	chr17:46046600-46047600	Weak transcription	Hela-S3	cervix
47	chr17:46047000-46047400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:46047000-46047600	Enhancers	K562	blood
49	chr17:46047000-46047800	Enhancers	Gastric	stomach
50	chr17:46047000-46049400	Active TSS	Rectal Smooth Muscle	rectum

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