Variant report

Variant	rs55975153
Chromosome Location	chr12:50505006-50505007
allele	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	POLR2A	chr12:50504924-50506691	H1-neurons	neurons:	n/a	n/a
2	ZBTB7A	chr12:50504807-50505030	K562	blood:	n/a	n/a
3	POLR2A	chr12:50503933-50506466	GM19099	blood:	n/a	n/a
4	CTCF	chr12:50504900-50505050	AG04449	skin:	n/a	n/a
5	STAT3	chr12:50505000-50505200	MCF10A-Er-Src	breast:	n/a	chr12:50505085-50505096
6	MAX	chr12:50504378-50506841	ECC-1	luminal epithelium:	n/a	n/a
7	MAZ	chr12:50503927-50506432	Hela-S3	cervix:	n/a	n/a
8	MAZ	chr12:50503965-50506167	K562	blood:	n/a	n/a
9	CHD2	chr12:50504889-50505142	GM12878	blood:	n/a	n/a
10	CTCF	chr12:50504940-50505090	AG10803	skin:	n/a	n/a
11	RFX5	chr12:50502880-50507261	SK-N-SH	brain:	n/a	n/a
12	MAX	chr12:50504603-50505060	HepG2	liver:	n/a	n/a
13	CREB1	chr12:50504919-50506630	HepG2	liver:	n/a	chr12:50505568-50505581 chr12:50505568-50505581
14	ZBTB7A	chr12:50504571-50505716	ECC-1	luminal epithelium:	n/a	chr12:50505514-50505523 chr12:50505286-50505295
15	CTCF	chr12:50504900-50505050	NHDF-neo	bronchial:	n/a	n/a
16	SMC3	chr12:50503993-50505021	Hela-S3	cervix:	n/a	n/a
17	RFX5	chr12:50503903-50506209	GM12878	blood:	n/a	n/a
18	CTCF	chr12:50504994-50505700	K562	blood:	n/a	chr12:50505286-50505302 chr12:50505507-50505523 chr12:50505506-50505524 chr12:50505287-50505300
19	CTCF	chr12:50504224-50506720	A549	lung:	n/a	chr12:50505286-50505302 chr12:50505507-50505523 chr12:50505506-50505524 chr12:50505287-50505300
20	NFYB	chr12:50504576-50506258	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr12:50504352-50505032	ECC-1	luminal epithelium:	n/a	n/a
22	GTF2F1	chr12:50503988-50506506	Hela-S3	cervix:	n/a	n/a
23	EBF1	chr12:50504545-50505007	GM12878	blood:	n/a	n/a
24	NR3C1	chr12:50504667-50505249	A549	lung:	n/a	n/a
25	MXI1	chr12:50504237-50505047	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr12:50504816-50506088	MCF-7	breast:	n/a	chr12:50505286-50505302 chr12:50505507-50505523 chr12:50505506-50505524 chr12:50505287-50505300
27	POLR2A	chr12:50503948-50506522	GM18505	blood:	n/a	n/a
28	CTCF	chr12:50505000-50505150	HRE	kidney:	n/a	n/a
29	MXI1	chr12:50504775-50507255	SK-N-SH	brain:	n/a	n/a
30	SMARCB1	chr12:50503334-50506550	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:50503976-50506528	Raji	blood:	n/a	n/a
32	RELA	chr12:50504050-50506645	GM15510	blood:	n/a	n/a
33	CTCF	chr12:50504940-50505090	HCM	heart:	n/a	n/a
34	TCF12	chr12:50504096-50505018	ECC-1	luminal epithelium:	n/a	n/a
35	MTA3	chr12:50503671-50506637	GM12878	blood:	n/a	n/a
36	RELA	chr12:50504907-50506412	GM10847	blood:	n/a	n/a
37	MAZ	chr12:50503952-50506200	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:50503776-50506609	Hela-S3	cervix:	n/a	n/a
39	NR2F2	chr12:50503918-50505152	MCF-7	breast:	n/a	n/a
40	EBF1	chr12:50503794-50505097	GM12878	blood:	n/a	n/a
41	CTCF	chr12:50505001-50505988	HCT-116	colon:	n/a	chr12:50505286-50505302 chr12:50505507-50505523 chr12:50505506-50505524 chr12:50505287-50505300
42	POLR2A	chr12:50503958-50505094	GM18526	blood:	n/a	n/a
43	POLR2A	chr12:50503834-50505008	HepG2	liver:	n/a	n/a
44	NR3C1	chr12:50504811-50505060	A549	lung:	n/a	n/a
45	MAX	chr12:50504868-50505244	K562	blood:	n/a	n/a
46	SMC3	chr12:50504937-50506874	SK-N-SH	brain:	n/a	chr12:50505508-50505522
47	CTCF	chr12:50504900-50505050	AG10803	skin:	n/a	n/a
48	POLR2A	chr12:50503864-50505094	Hela-S3	cervix:	n/a	n/a
49	RFX5	chr12:50503133-50506733	IMR90	lung:	n/a	n/a
50	ZKSCAN1	chr12:50503946-50505042	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50503774..50506593-chr2:166650902..166652995,2	MCF-7	breast:
2	chr12:50504882..50505728-chr12:50568694..50569880,4	MCF-7	breast:
3	chr12:50504921..50507290-chr12:50793420..50795913,2	K562	blood:
4	chr12:50504614..50508392-chr12:50676689..50680044,5	K562	blood:
5	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
6	chr12:50491501..50494072-chr12:50502085..50505008,3	K562	blood:
7	chr12:50504921..50507362-chr12:50794413..50796105,2	K562	blood:
8	chr12:50504135..50506264-chr12:50615508..50617145,2	K562	blood:
9	chr12:50478595..50483647-chr12:50502911..50507517,7	K562	blood:
10	chr1:153949703..153950297-chr12:50504586..50505542,2	Hela-S3	cervix:
11	chr12:50504583..50505288-chr15:59397225..59397744,2	Hela-S3	cervix:
12	chr12:50134183..50135831-chr12:50504154..50505944,2	K562	blood:
13	chr12:50504763..50507079-chr12:50528230..50529820,2	MCF-7	breast:
14	chr12:50504323..50505125-chr15:65588171..65588889,2	Hela-S3	cervix:
15	chr12:50504059..50507401-chr12:50559290..50562708,7	K562	blood:
16	chr12:50503326..50508590-chr12:50559314..50563839,9	MCF-7	breast:
17	chr12:50504767..50505346-chrX:107334434..107334993,2	Hela-S3	cervix:
18	chr12:50503967..50508677-chr12:50559559..50562905,8	MCF-7	breast:
19	chr12:50499334..50507442-chr12:50559441..50562987,11	K562	blood:

Variant related genes	Relation type
COX14	TF binding region
ENSG00000272368	TF binding region
ENSG00000143543	Chromatin interaction
ENSG00000272654	Chromatin interaction
ENSG00000101843	Chromatin interaction
ENSG00000157456	Chromatin interaction
ENSG00000101844	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000203433	Chromatin interaction
ENSG00000115339	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000235192	Chromatin interaction
ENSG00000139624	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs74090026	0.86[AFR][1000 genomes]
rs74090049	0.86[AFR][1000 genomes]
rs74090055	1.00[AFR][1000 genomes]
rs74090059	1.00[AFR][1000 genomes]
rs74090080	1.00[AFR][1000 genomes]
rs7969938	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50494000-50505200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:50495800-50505200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:50500600-50505200	Genic enhancers	Fetal Intestine Small	intestine
4	chr12:50500800-50505200	Enhancers	Psoas Muscle	Psoas
5	chr12:50501600-50505200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:50502000-50505600	Enhancers	Stomach Mucosa	stomach
7	chr12:50502600-50505800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:50502800-50505200	Enhancers	Fetal Muscle Leg	muscle
9	chr12:50503000-50505200	Flanking Active TSS	Liver	Liver
10	chr12:50503000-50505200	Enhancers	Brain Substantia Nigra	brain
11	chr12:50503000-50505200	Enhancers	Esophagus	oesophagus
12	chr12:50503000-50505200	Enhancers	Fetal Muscle Trunk	muscle
13	chr12:50503000-50505200	Enhancers	Left Ventricle	heart
14	chr12:50503000-50505200	Enhancers	Pancreas	Pancrea
15	chr12:50503000-50505200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr12:50503000-50505200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:50503000-50505400	Enhancers	Placenta	Placenta
18	chr12:50503000-50505400	Flanking Active TSS	Hela-S3	cervix
19	chr12:50503000-50506800	Active TSS	Rectal Smooth Muscle	rectum
20	chr12:50503200-50505200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:50503200-50505200	Enhancers	Lung	lung
22	chr12:50503200-50505200	Enhancers	Right Atrium	heart
23	chr12:50503200-50505800	Enhancers	Fetal Thymus	thymus
24	chr12:50503400-50505200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:50503400-50505200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:50503400-50505200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr12:50503400-50505400	Enhancers	Aorta	Aorta
28	chr12:50503400-50505400	Flanking Active TSS	Colonic Mucosa	Colon
29	chr12:50503400-50505400	Enhancers	NHDF-Ad	bronchial
30	chr12:50503600-50505200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr12:50503600-50505200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:50503600-50505200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:50503600-50505200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr12:50503600-50505200	Enhancers	Fetal Intestine Large	intestine
35	chr12:50503600-50505600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:50503600-50505600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr12:50503800-50505200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:50503800-50505200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:50503800-50505200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:50503800-50505200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr12:50503800-50505200	Flanking Active TSS	GM12878-XiMat	blood
42	chr12:50503800-50505200	Flanking Active TSS	K562	blood
43	chr12:50503800-50505400	Flanking Active TSS	A549	lung
44	chr12:50503800-50505600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr12:50504000-50505200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:50504000-50505200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr12:50504000-50505200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:50504000-50505200	Enhancers	Fetal Stomach	stomach
49	chr12:50504000-50505200	Flanking Active TSS	HSMM	muscle
50	chr12:50504000-50505600	Enhancers	Gastric	stomach

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