Variant report

Variant	rs35848720
Chromosome Location	chr17:46056481-46056482
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	SMC3	chr17:46055523-46058664	SK-N-SH	brain:	n/a	chr17:46058259-46058269 chr17:46055894-46055908 chr17:46057121-46057129
2	CTCF	chr17:46055581-46056732	SK-N-SH	brain:	n/a	chr17:46055894-46055915 chr17:46055895-46055908 chr17:46055897-46055905 chr17:46055895-46055908 chr17:46055893-46055909 chr17:46055892-46055910
3	RAD21	chr17:46055608-46058810	SK-N-SH	brain:	n/a	chr17:46055897-46055906 chr17:46058189-46058201 chr17:46056305-46056315 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908 chr17:46058259-46058269

No.	Distal block	Cell Line	Cell type
1	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:
2	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
3	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
4	chr17:46034267..46036157-chr17:46054956..46057577,2	MCF-7	breast:
5	chr17:46046859..46048450-chr17:46055513..46058232,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000167183	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12939977	0.81[AFR][1000 genomes]
rs12941306	1.00[AFR][1000 genomes];1.00[AMR][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	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]
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	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:3 , 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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 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	chr17:46049600-46059600	Weak transcription	Fetal Heart	heart
2	chr17:46049800-46058200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
4	chr17:46050200-46060400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr17:46050200-46060400	Strong transcription	Osteobl	bone
6	chr17:46050200-46061800	Strong transcription	NHLF	lung
7	chr17:46050200-46062000	Strong transcription	NHEK	skin
8	chr17:46050200-46062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
12	chr17:46050400-46056800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr17:46050400-46058000	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr17:46050400-46060800	Strong transcription	Ovary	ovary
15	chr17:46050400-46061000	Strong transcription	A549	lung
16	chr17:46050400-46061200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:46050400-46061400	Strong transcription	HepG2	liver
18	chr17:46050400-46062000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:46050400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr17:46050600-46057000	Strong transcription	Dnd41	blood
22	chr17:46050600-46058000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr17:46050600-46061800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr17:46050600-46062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr17:46050600-46062200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr17:46050800-46057200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:46050800-46058000	Strong transcription	Brain Cingulate Gyrus	brain
30	chr17:46050800-46059000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr17:46050800-46059200	Strong transcription	Liver	Liver
32	chr17:46050800-46059200	Strong transcription	Spleen	Spleen
33	chr17:46050800-46059600	Strong transcription	Brain Anterior Caudate	brain
34	chr17:46050800-46060000	Strong transcription	Brain Angular Gyrus	brain
35	chr17:46050800-46060200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr17:46050800-46060200	Strong transcription	Adipose Nuclei	Adipose
37	chr17:46050800-46060200	Strong transcription	Gastric	stomach
38	chr17:46050800-46060800	Strong transcription	Lung	lung
39	chr17:46050800-46061000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr17:46050800-46061200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr17:46050800-46061600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:46050800-46061600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr17:46050800-46061800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:46050800-46062000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr17:46050800-46062000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr17:46050800-46062200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr17:46050800-46062400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr17:46050800-46062600	Strong transcription	Fetal Intestine Small	intestine
49	chr17:46050800-46062800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr17:46050800-46063000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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