Variant report

Variant	rs17879452
Chromosome Location	chr13:96330420-96330421
allele	A/G
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	MXI1	chr13:96328102-96331205	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr13:96327871-96330548	PBDE	blood:	n/a	n/a
3	ZNF384	chr13:96330420-96330789	GM12878	blood:	n/a	n/a
4	E2F4	chr13:96330313-96330612	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr13:96328269-96330465	GM12891	blood:	n/a	n/a
6	SIN3A	chr13:96330046-96330483	GM12878	blood:	n/a	n/a
7	MYC	chr13:96328275-96330568	NB4	blood:	n/a	chr13:96329358-96329368
8	RUNX3	chr13:96328348-96330569	GM12878	blood:	n/a	chr13:96330200-96330209 chr13:96330200-96330209
9	USF2	chr13:96330094-96330490	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr13:96328302-96330598	GM12878	blood:	n/a	n/a
11	POLR2A	chr13:96330068-96330525	K562	blood:	n/a	n/a
12	STAT3	chr13:96330393-96330481	MCF10A-Er-Src	breast:	n/a	n/a
13	ARID3A	chr13:96330245-96330651	K562	blood:	n/a	n/a
14	SIN3A	chr13:96328335-96330554	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAZ	chr13:96328849-96330630	GM12878	blood:	n/a	chr13:96329358-96329368
16	MYC	chr13:96330086-96330468	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr13:96330300-96330450	AG09319	gingival:	n/a	n/a
18	POLR2A	chr13:96328280-96330829	GM12878	blood:	n/a	n/a
19	CHD1	chr13:96330288-96330572	H1-hESC	embryonic stem cell:	n/a	n/a
20	KAP1	chr13:96330325-96330711	K562	blood:	n/a	n/a
21	STAT3	chr13:96330379-96330488	MCF10A-Er-Src	breast:	n/a	n/a
22	RCOR1	chr13:96330248-96330448	K562	blood:	n/a	n/a
23	MXI1	chr13:96328260-96330830	IMR90	lung:	n/a	n/a
24	TBP	chr13:96330090-96330499	Hela-S3	cervix:	n/a	n/a
25	CHD1	chr13:96329293-96330667	IMR90	lung:	n/a	n/a
26	POLR2A	chr13:96327481-96330995	MCF10A-Er-Src	breast:	n/a	n/a
27	UBTF	chr13:96328270-96330553	K562	blood:	n/a	n/a
28	MAZ	chr13:96328362-96330954	IMR90	lung:	n/a	chr13:96329358-96329368
29	RFX5	chr13:96330113-96330646	Hela-S3	cervix:	n/a	n/a
30	ZNF384	chr13:96330399-96331030	K562	blood:	n/a	n/a
31	POLR2A	chr13:96328390-96330496	K562	blood:	n/a	n/a
32	MYC	chr13:96330107-96330620	MCF10A-Er-Src	breast:	n/a	n/a
33	GTF2F1	chr13:96329919-96330575	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr13:96328039-96330618	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr13:96330400-96330550	HepG2	liver:	n/a	n/a
36	FOS	chr13:96330261-96330586	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr13:96327079-96330590	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr13:96330373-96330571	MCF10A-Er-Src	breast:	n/a	n/a
39	MAX	chr13:96328252-96330600	Hela-S3	cervix:	n/a	chr13:96329358-96329368
40	POLR2A	chr13:96329911-96330424	Hela-S3	cervix:	n/a	n/a
41	FOS	chr13:96330223-96330557	MCF10A-Er-Src	breast:	n/a	n/a
42	JUND	chr13:96330250-96330644	K562	blood:	n/a	n/a
43	BHLHE40	chr13:96330095-96330518	K562	blood:	n/a	n/a
44	MXI1	chr13:96328340-96330536	Hela-S3	cervix:	n/a	n/a
45	MYC	chr13:96328442-96330474	K562	blood:	n/a	chr13:96329358-96329368
46	MAX	chr13:96328300-96330660	NB4	blood:	n/a	chr13:96329358-96329368
47	RUNX3	chr13:96329892-96330530	GM12878	blood:	n/a	chr13:96330200-96330209 chr13:96330200-96330209

No.	Distal block	Cell Line	Cell type
1	chr13:96329213..96330784-chr13:96346091..96348298,2	MCF-7	breast:
2	chr13:96327826..96331109-chr13:96365382..96368282,3	MCF-7	breast:
3	chr13:96330224..96330806-chr2:182757051..182757713,2	Hela-S3	cervix:

Variant related genes	Relation type
DNAJC3-AS1	TF binding region
ENSG00000138434	Chromatin interaction
ENSG00000232373	Chromatin interaction
ENSG00000227714	Chromatin interaction
ENSG00000251901	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17878379	0.80[AFR][1000 genomes]
rs17878553	0.80[AFR][1000 genomes]
rs17878672	0.80[AFR][1000 genomes]
rs17878908	0.80[AFR][1000 genomes]
rs17879622	0.80[AFR][1000 genomes]
rs17879680	0.80[AFR][1000 genomes]
rs17880149	0.80[AFR][1000 genomes]
rs17882141	0.80[AFR][1000 genomes]
rs17882315	0.80[AFR][1000 genomes]
rs17882465	0.80[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3406527	chr13:96328176-96330724	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96325600-96332400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:96327000-96330600	Active TSS	Duodenum Mucosa	Duodenum
3	chr13:96327000-96330800	Active TSS	Fetal Intestine Large	intestine
4	chr13:96327000-96331000	Active TSS	K562	blood
5	chr13:96327000-96331800	Active TSS	GM12878-XiMat	blood
6	chr13:96327200-96331000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr13:96327400-96331000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr13:96327600-96330600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:96327600-96330800	Active TSS	Fetal Intestine Small	intestine
10	chr13:96327600-96331000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:96327600-96331000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:96327600-96331000	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr13:96327600-96331000	Active TSS	HMEC	breast
14	chr13:96327600-96331200	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr13:96327600-96331400	Active TSS	Right Ventricle	heart
16	chr13:96327800-96331000	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr13:96328000-96330600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr13:96328000-96330600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr13:96328000-96330600	Active TSS	Psoas Muscle	Psoas
20	chr13:96328000-96330600	Active TSS	Stomach Smooth Muscle	stomach
21	chr13:96328000-96330800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr13:96328000-96330800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr13:96328000-96330800	Active TSS	NHEK	skin
24	chr13:96328000-96331000	Active TSS	Colon Smooth Muscle	Colon
25	chr13:96328000-96331000	Active TSS	A549	lung
26	chr13:96328000-96331000	Active TSS	Hela-S3	cervix
27	chr13:96328000-96331000	Active TSS	HSMMtube	muscle
28	chr13:96328000-96331200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr13:96328000-96331200	Active TSS	Colonic Mucosa	Colon
30	chr13:96328000-96331200	Active TSS	Ovary	ovary
31	chr13:96328000-96332000	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr13:96328200-96330600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr13:96328200-96330600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr13:96328200-96330600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr13:96328200-96330600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr13:96328200-96330600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr13:96328200-96330600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr13:96328200-96330600	Active TSS	Stomach Mucosa	stomach
39	chr13:96328200-96330800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr13:96328200-96330800	Active TSS	Fetal Stomach	stomach
41	chr13:96328200-96331000	Active TSS	Brain Substantia Nigra	brain
42	chr13:96328200-96331000	Active TSS	NHLF	lung
43	chr13:96328200-96331200	Active TSS	Fetal Muscle Trunk	muscle
44	chr13:96328200-96331200	Active TSS	HSMM	muscle
45	chr13:96328200-96331400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:96328200-96331400	Active TSS	Aorta	Aorta
47	chr13:96328200-96331400	Active TSS	Left Ventricle	heart
48	chr13:96328200-96331400	Active TSS	Pancreas	Pancrea
49	chr13:96328400-96330600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:96328400-96330600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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