Variant report

Variant	rs12939977
Chromosome Location	chr17:46056120-46056121
allele	A/C/G/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	BRCA1	chr17:46056117-46056139	GM12878	blood:	n/a	n/a
3	RAD21	chr17:46055692-46056275	MCF-7	breast:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
4	RAD21	chr17:46055671-46056214	A549	lung:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
5	SMC3	chr17:46055754-46056122	K562	blood:	n/a	chr17:46055894-46055908
6	MAZ	chr17:46055705-46056447	IMR90	lung:	n/a	n/a
7	RAD21	chr17:46055640-46056375	SK-N-SH_RA	brain:	n/a	chr17:46055897-46055906 chr17:46056305-46056315 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
8	CTCF	chr17:46055599-46056420	A549	lung:	n/a	chr17:46055894-46055915 chr17:46055895-46055908 chr17:46055897-46055905 chr17:46055895-46055908 chr17:46055893-46055909 chr17:46055892-46055910
9	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
10	RUNX3	chr17:46055731-46056140	GM12878	blood:	n/a	n/a
11	RAD21	chr17:46055702-46056144	IMR90	lung:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
12	RAD21	chr17:46055693-46056288	HCT-116	colon:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
13	CTCF	chr17:46055633-46056275	HCT-116	colon:	n/a	chr17:46055894-46055915 chr17:46055895-46055908 chr17:46055897-46055905 chr17:46055895-46055908 chr17:46055893-46055909 chr17:46055892-46055910
14	ATF2	chr17:46055721-46056123	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr17:46055692-46056127	H1-hESC	embryonic stem cell:	n/a	chr17:46055894-46055915 chr17:46055895-46055908 chr17:46055897-46055905 chr17:46055895-46055908 chr17:46055893-46055909 chr17:46055892-46055910
16	RAD21	chr17:46055696-46056259	A549	lung:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
17	RAD21	chr17:46055736-46056153	GM12878	blood:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
18	SMC3	chr17:46055725-46056203	GM12878	blood:	n/a	chr17:46055894-46055908
19	RAD21	chr17:46055732-46056124	Hela-S3	cervix:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
20	RAD21	chr17:46055668-46056263	SK-N-SH_RA	brain:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
21	CTCF	chr17:46055593-46056150	A549	lung:	n/a	chr17:46055894-46055915 chr17:46055895-46055908 chr17:46055897-46055905 chr17:46055895-46055908 chr17:46055893-46055909 chr17:46055892-46055910
22	CTCF	chr17:46055690-46056222	MCF-7	breast:	n/a	chr17:46055894-46055915 chr17:46055895-46055908 chr17:46055897-46055905 chr17:46055895-46055908 chr17:46055893-46055909 chr17:46055892-46055910
23	RAD21	chr17:46055678-46056156	HepG2	liver:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
24	CTCF	chr17:46055709-46056214	MCF-7	breast:	n/a	chr17:46055894-46055915 chr17:46055895-46055908 chr17:46055897-46055905 chr17:46055895-46055908 chr17:46055893-46055909 chr17:46055892-46055910
25	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
26	RAD21	chr17:46055697-46056324	HCT-116	colon:	n/a	chr17:46055897-46055906 chr17:46056305-46056315 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
27	RAD21	chr17:46055667-46056237	ECC-1	luminal epithelium:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
28	RAD21	chr17:46055653-46056273	H1-hESC	embryonic stem cell:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
29	RAD21	chr17:46055708-46056153	H1-hESC	embryonic stem cell:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
30	CHD1	chr17:46055887-46056146	GM12878	blood:	n/a	n/a
31	FOXM1	chr17:46055677-46056132	GM12878	blood:	n/a	n/a
32	RAD21	chr17:46055691-46056312	MCF-7	breast:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908
33	RAD21	chr17:46055687-46056173	ECC-1	luminal epithelium:	n/a	chr17:46055897-46055906 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908

No.	Distal block	Cell Line	Cell type
1	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
2	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
3	chr17:46034267..46036157-chr17:46054956..46057577,2	MCF-7	breast:
4	chr17:46046859..46048450-chr17:46055513..46058232,2	K562	blood:
5	chr17:46024543..46026331-chr17:46053891..46056374,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000167183	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000264019	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12935964	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs12941306	0.81[AFR][1000 genomes]
rs12947966	0.81[AFR][1000 genomes]
rs12948207	0.81[AFR][1000 genomes]
rs34358803	0.81[AFR][1000 genomes]
rs34601263	0.81[AFR][1000 genomes]
rs34958507	0.81[AFR][1000 genomes]
rs35751035	0.81[AFR][1000 genomes]
rs35766594	0.81[AFR][1000 genomes]
rs35795560	0.81[AFR][1000 genomes]
rs35848720	0.81[AFR][1000 genomes]
rs36059789	0.81[AFR][1000 genomes]
rs59727791	0.81[AFR][1000 genomes]
rs71369826	1.00[AMR][1000 genomes]
rs71377331	0.81[AFR][1000 genomes]
rs71377332	0.81[AFR][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	chr17:46049600-46056200	Weak transcription	Psoas Muscle	Psoas
2	chr17:46049600-46059600	Weak transcription	Fetal Heart	heart
3	chr17:46049800-46058200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
5	chr17:46050000-46056200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:46050200-46060400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr17:46050200-46060400	Strong transcription	Osteobl	bone
8	chr17:46050200-46061800	Strong transcription	NHLF	lung
9	chr17:46050200-46062000	Strong transcription	NHEK	skin
10	chr17:46050200-46062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
14	chr17:46050400-46056800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:46050400-46058000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr17:46050400-46060800	Strong transcription	Ovary	ovary
17	chr17:46050400-46061000	Strong transcription	A549	lung
18	chr17:46050400-46061200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:46050400-46061400	Strong transcription	HepG2	liver
20	chr17:46050400-46062000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:46050400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr17:46050600-46056200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr17:46050600-46057000	Strong transcription	Dnd41	blood
25	chr17:46050600-46058000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr17:46050600-46061800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr17:46050600-46062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr17:46050600-46062200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr17:46050800-46057200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:46050800-46058000	Strong transcription	Brain Cingulate Gyrus	brain
33	chr17:46050800-46059000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr17:46050800-46059200	Strong transcription	Liver	Liver
35	chr17:46050800-46059200	Strong transcription	Spleen	Spleen
36	chr17:46050800-46059600	Strong transcription	Brain Anterior Caudate	brain
37	chr17:46050800-46060000	Strong transcription	Brain Angular Gyrus	brain
38	chr17:46050800-46060200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:46050800-46060200	Strong transcription	Adipose Nuclei	Adipose
40	chr17:46050800-46060200	Strong transcription	Gastric	stomach
41	chr17:46050800-46060800	Strong transcription	Lung	lung
42	chr17:46050800-46061000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr17:46050800-46061200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr17:46050800-46061600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:46050800-46061600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr17:46050800-46061800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:46050800-46062000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr17:46050800-46062000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr17:46050800-46062200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr17:46050800-46062400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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