Variant report

Variant	rs556203676
Chromosome Location	chr12:50478853-50478854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:545)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:545 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:50478749-50479026	GM10266	blood:	n/a	chr12:50478890-50478903
2	ELF1	chr12:50478610-50479144	A549	lung:	n/a	n/a
3	CTCF	chr12:50478820-50478970	GM12878	blood:	n/a	chr12:50478890-50478903
4	CTCF	chr12:50478800-50478950	AG09319	gingival:	n/a	chr12:50478890-50478903
5	CTCF	chr12:50478662-50479063	HepG2	liver:	n/a	chr12:50478890-50478903
6	GABPA	chr12:50478751-50479365	GM12878	blood:	n/a	n/a
7	GTF2F1	chr12:50478682-50478999	K562	blood:	n/a	n/a
8	FOS	chr12:50478800-50479013	MCF10A-Er-Src	breast:	n/a	n/a
9	TAF1	chr12:50478661-50479388	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:50478628-50479735	H1-neurons	neurons:	n/a	n/a
11	SIN3A	chr12:50478566-50479817	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr12:50478668-50479376	K562	blood:	n/a	chr12:50479142-50479162
13	CTCF	chr12:50478740-50478890	HA-sp	spinal cord:	n/a	n/a
14	CTCF	chr12:50478737-50479025	ProgFib	skin:	n/a	chr12:50478890-50478903
15	EGR1	chr12:50478681-50479069	K562	blood:	n/a	chr12:50478900-50478914
16	FOXM1	chr12:50478527-50479141	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:50478645-50479341	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr12:50478840-50478990	NHEK	skin:	n/a	chr12:50478890-50478903
19	ZBTB7A	chr12:50478675-50479416	K562	blood:	n/a	n/a
20	FOXM1	chr12:50478568-50479229	GM12878	blood:	n/a	n/a
21	MAX	chr12:50478438-50479186	K562	blood:	n/a	chr12:50478768-50478777
22	GABPA	chr12:50478758-50479385	HepG2	liver:	n/a	n/a
23	TAF1	chr12:50478577-50479638	ECC-1	luminal epithelium:	n/a	n/a
24	SIN3AK20	chr12:50478783-50479067	HepG2	liver:	n/a	n/a
25	GABPA	chr12:50478684-50479326	Hela-S3	cervix:	n/a	n/a
26	JUN	chr12:50478693-50479024	K562	blood:	n/a	n/a
27	POLR2A	chr12:50478656-50479513	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr12:50478292-50479283	SK-N-SH	brain:	n/a	chr12:50478890-50478903
29	CTCF	chr12:50478752-50479049	GM12891	blood:	n/a	chr12:50478890-50478903
30	POLR2A	chr12:50478649-50478887	HepG2	liver:	n/a	n/a
31	YY1	chr12:50478713-50479051	HCT-116	colon:	n/a	n/a
32	MAX	chr12:50478730-50479232	H1-hESC	embryonic stem cell:	n/a	chr12:50478768-50478777
33	CTCF	chr12:50478693-50479102	IMR90	lung:	n/a	chr12:50478890-50478903
34	POLR2A	chr12:50478501-50479406	PFSK-1	brain:	n/a	n/a
35	ELF1	chr12:50478629-50479440	MCF-7	breast:	n/a	n/a
36	TAF1	chr12:50478642-50479464	H1-neurons	neurons:	n/a	n/a
37	MXI1	chr12:50478633-50479093	K562	blood:	n/a	n/a
38	YY1	chr12:50478644-50479414	SK-N-SH_RA	brain:	n/a	chr12:50479142-50479162
39	POLR2A	chr12:50478666-50479590	HepG2	liver:	n/a	n/a
40	PAX5	chr12:50478790-50479329	GM12892	blood:	n/a	n/a
41	POLR2A	chr12:50478671-50478863	H1-hESC	embryonic stem cell:	n/a	n/a
42	CREB1	chr12:50478593-50479176	H1-hESC	embryonic stem cell:	n/a	n/a
43	RUNX3	chr12:50478539-50479299	GM12878	blood:	n/a	n/a
44	ELK1	chr12:50478726-50479013	K562	blood:	n/a	n/a
45	CTCF	chr12:50478730-50478985	A549	lung:	n/a	chr12:50478890-50478903
46	POLR2A	chr12:50477999-50480078	HepG2	liver:	n/a	n/a
47	MAX	chr12:50478649-50479224	H1-hESC	embryonic stem cell:	n/a	chr12:50478768-50478777
48	YY1	chr12:50478770-50479323	HepG2	liver:	n/a	chr12:50479142-50479162
49	BCLAF1	chr12:50478566-50479193	GM12878	blood:	n/a	n/a
50	POLR2A	chr12:50478620-50479711	K562	blood:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50476634..50479276-chr12:50493202..50495258,2	K562	blood:
2	chr12:50477150..50481052-chr12:50559881..50562931,6	MCF-7	breast:
3	chr12:50478595..50483647-chr12:50502911..50507517,7	K562	blood:
4	chr12:50478513..50480166-chr12:50489047..50490966,2	K562	blood:
5	chr12:50477499..50479020-chr12:50528748..50530881,2	MCF-7	breast:
6	chr12:50477720..50479464-chr12:50594213..50596665,2	MCF-7	breast:
7	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
8	chr12:50472028..50474859-chr12:50477717..50480636,3	MCF-7	breast:
9	chr12:50477580..50479686-chr17:62501151..62502654,2	MCF-7	breast:
10	chr12:50478149..50480392-chr17:58677532..58679268,2	MCF-7	breast:
11	chr12:50477670..50481382-chr12:50495555..50500836,7	K562	blood:
12	chr12:50478449..50481902-chr12:50536030..50539935,3	MCF-7	breast:
13	chr12:50475132..50479699-chr12:50479828..50484275,5	K562	blood:
14	chr12:50477885..50480264-chr12:50559751..50562542,2	K562	blood:
15	chr12:50478759..50480659-chr12:50481009..50483998,3	K562	blood:
16	chr12:50477576..50479559-chr12:50526628..50528314,2	MCF-7	breast:
17	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
18	chr12:50469904..50470842-chr12:50478448..50479302,2	K562	blood:
19	chr12:50478583..50479243-chr3:179280120..179280858,2	Hela-S3	cervix:
20	chr12:50477100..50479136-chr12:50582674..50585443,2	K562	blood:
21	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
22	chr12:49524766..49526462-chr12:50478450..50480251,2	MCF-7	breast:
23	chr12:50461826..50464798-chr12:50477927..50479451,2	K562	blood:
24	chr12:50477688..50480373-chr12:50497434..50499573,3	K562	blood:
25	chr12:50478705..50480450-chr12:50534679..50536447,2	MCF-7	breast:
26	chr12:50477178..50480105-chr12:50648113..50650406,2	K562	blood:
27	chr12:50235441..50237993-chr12:50478392..50480338,2	K562	blood:
28	chr12:50464456..50466840-chr12:50477683..50480596,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMARCD1	TF binding region
ENSG00000258017	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000257298	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000170836	Chromatin interaction
ENSG00000136518	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000212496	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3437172	chr12:50478110-50480658	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50477800-50479400	Active TSS	Dnd41	blood
2	chr12:50478000-50479600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr12:50478000-50480200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:50478200-50479000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr12:50478200-50479000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:50478200-50479400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:50478200-50479400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:50478200-50479600	Active TSS	Aorta	Aorta
9	chr12:50478200-50479600	Active TSS	Colonic Mucosa	Colon
10	chr12:50478200-50479600	Active TSS	Colon Smooth Muscle	Colon
11	chr12:50478200-50479600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:50478200-50479600	Active TSS	Pancreas	Pancrea
13	chr12:50478200-50479600	Active TSS	A549	lung
14	chr12:50478200-50479600	Active TSS	HepG2	liver
15	chr12:50478200-50479600	Active TSS	HMEC	breast
16	chr12:50478200-50479600	Active TSS	HSMM	muscle
17	chr12:50478200-50479600	Active TSS	HSMMtube	muscle
18	chr12:50478200-50479800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr12:50478200-50479800	Active TSS	Fetal Lung	lung
20	chr12:50478200-50479800	Active TSS	Left Ventricle	heart
21	chr12:50478200-50479800	Active TSS	Right Atrium	heart
22	chr12:50478200-50479800	Active TSS	Stomach Smooth Muscle	stomach
23	chr12:50478200-50479800	Active TSS	GM12878-XiMat	blood
24	chr12:50478200-50479800	Active TSS	NHEK	skin
25	chr12:50478200-50480000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr12:50478200-50480000	Active TSS	Fetal Brain Female	brain
27	chr12:50478200-50480000	Active TSS	Fetal Kidney	kidney
28	chr12:50478200-50480000	Active TSS	Psoas Muscle	Psoas
29	chr12:50478200-50480200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr12:50478200-50480200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:50478200-50480200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:50478200-50480200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr12:50478200-50480200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr12:50478200-50480200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:50478200-50480200	Active TSS	Rectal Smooth Muscle	rectum
36	chr12:50478200-50480200	Active TSS	NHLF	lung
37	chr12:50478200-50480400	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr12:50478400-50479000	Active TSS	Stomach Mucosa	stomach
39	chr12:50478400-50479400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:50478400-50479400	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr12:50478400-50479400	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr12:50478400-50479400	Active TSS	Liver	Liver
43	chr12:50478400-50479400	Active TSS	Fetal Muscle Trunk	muscle
44	chr12:50478400-50479600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr12:50478400-50479600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:50478400-50479600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:50478400-50479600	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr12:50478400-50479600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr12:50478400-50479600	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr12:50478400-50479600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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