Variant report

Variant	rs556601369
Chromosome Location	chr12:30907972-30907973
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	CTCF	chr12:30907725-30908255	GM12892	blood:	n/a	n/a
2	HEY1	chr12:30907511-30908305	K562	blood:	n/a	chr12:30907745-30907760 chr12:30907836-30907851 chr12:30907703-30907718 chr12:30907888-30907903 chr12:30907550-30907565
3	BACH1	chr12:30907301-30908343	H1-hESC	embryonic stem cell:	n/a	n/a
4	BCLAF1	chr12:30907629-30908418	GM12878	blood:	n/a	chr12:30907647-30907656 chr12:30907644-30907653 chr12:30907701-30907714 chr12:30907706-30907719
5	GATA3	chr12:30907631-30908600	A549	lung:	n/a	n/a
6	POLR2A	chr12:30907586-30908417	SK-N-MC	brain:	n/a	n/a
7	CTCF	chr12:30907960-30908110	HA-sp	spinal cord:	n/a	n/a
8	POLR2A	chr12:30906969-30908372	Hela-S3	cervix:	n/a	n/a
9	BRCA1	chr12:30907912-30908264	Hela-S3	cervix:	n/a	n/a
10	ZBTB7A	chr12:30907104-30908415	ECC-1	luminal epithelium:	n/a	n/a
11	ELF1	chr12:30907653-30908375	GM12878	blood:	n/a	chr12:30907834-30907846 chr12:30907696-30907708
12	POLR2A	chr12:30907578-30908246	GM12892	blood:	n/a	n/a
13	POLR2A	chr12:30907278-30908386	A549	lung:	n/a	n/a
14	POLR2A	chr12:30906990-30908446	Hela-S3	cervix:	n/a	n/a
15	YY1	chr12:30907646-30908219	GM12878	blood:	n/a	chr12:30907705-30907719 chr12:30907704-30907715 chr12:30907832-30907846 chr12:30907701-30907715
16	CTCF	chr12:30907960-30908110	GM12865	blood:	n/a	n/a
17	CTCF	chr12:30907860-30908010	GM12873	blood:	n/a	n/a
18	MYC	chr12:30907818-30908079	K562	blood:	n/a	chr12:30907833-30907843 chr12:30907901-30907910
19	FOSL1	chr12:30907697-30908277	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:30907275-30908403	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:30907270-30908334	A549	lung:	n/a	n/a
22	MAX	chr12:30907565-30908490	SK-N-SH	brain:	n/a	chr12:30907833-30907843 chr12:30907901-30907910
23	CTCF	chr12:30907896-30908167	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr12:30907912-30908264	A549	lung:	n/a	chr12:30907993-30908000
25	MYC	chr12:30907539-30908580	A549	lung:	n/a	chr12:30907833-30907843 chr12:30907901-30907910
26	E2F6	chr12:30907771-30908348	A549	lung:	n/a	chr12:30908309-30908316
27	POLR2A	chr12:30907157-30908351	K562	blood:	n/a	n/a
28	USF1	chr12:30907906-30908371	H1-hESC	embryonic stem cell:	n/a	chr12:30907990-30908006
29	CTCF	chr12:30907960-30908110	HMEC	breast:	n/a	n/a
30	SIN3AK20	chr12:30907560-30908146	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr12:30907909-30908191	A549	lung:	n/a	n/a
32	CBX3	chr12:30907929-30908168	K562	blood:	n/a	n/a
33	ZNF143	chr12:30907644-30908255	K562	blood:	n/a	n/a
34	POLR2A	chr12:30907571-30908324	HepG2	liver:	n/a	n/a
35	RELA	chr12:30907506-30908470	GM18951	blood:	n/a	n/a
36	TCF12	chr12:30907668-30908495	ECC-1	luminal epithelium:	n/a	chr12:30907993-30908000
37	POLR2A	chr12:30906381-30908438	HepG2	liver:	n/a	n/a
38	MXI1	chr12:30906275-30908913	IMR90	lung:	n/a	n/a
39	NR2F2	chr12:30907738-30908374	K562	blood:	n/a	n/a
40	GATA3	chr12:30907730-30908549	MCF-7	breast:	n/a	n/a
41	CTCF	chr12:30907900-30908211	GM19239	blood:	n/a	n/a
42	TCF12	chr12:30907846-30908302	H1-hESC	embryonic stem cell:	n/a	chr12:30907993-30908000
43	CEBPB	chr12:30907595-30908867	Hela-S3	cervix:	n/a	chr12:30908831-30908844
44	SMC3	chr12:30906877-30908508	Hela-S3	cervix:	n/a	n/a
45	EP300	chr12:30907675-30908264	T-47D	breast:	n/a	n/a
46	ELF1	chr12:30907720-30908301	HepG2	liver:	n/a	chr12:30907834-30907846
47	CTCF	chr12:30907761-30908252	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr12:30907495-30908545	K562	blood:	n/a	n/a
49	GABPA	chr12:30907835-30908250	A549	lung:	n/a	n/a
50	MAX	chr12:30906907-30908428	Hela-S3	cervix:	n/a	chr12:30907833-30907843 chr12:30907901-30907910

No.	Distal block	Cell Line	Cell type
1	chr12:30845389..30848478-chr12:30907681..30910609,3	K562	blood:
2	chr1:45187119..45187880-chr12:30907389..30908146,2	HCT-116	colon:
3	chr1:161129253..161129757-chr12:30907615..30908521,2	Hela-S3	cervix:
4	chr12:30906304..30909589-chr12:30948532..30951386,3	K562	blood:
5	chr12:30907774..30908278-chr5:32585524..32586521,2	Hela-S3	cervix:
6	chr12:30907876..30908507-chr17:37356246..37356998,2	Hela-S3	cervix:
7	chr12:30902650..30905580-chr12:30906095..30908998,3	MCF-7	breast:
8	chr12:30907673..30908756-chr12:30947349..30948500,4	Hela-S3	cervix:

Variant related genes	Relation type
CAPRIN2	TF binding region
ENSG00000246331	TF binding region
ENSG00000110888	Chromatin interaction
ENSG00000113387	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000108298	Chromatin interaction
ENSG00000235884	Chromatin interaction
ENSG00000143258	Chromatin interaction
ENSG00000133704	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv3390684	chr12:30906885-30909083	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr12:30903800-30908400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:30905600-30908600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:30905800-30908800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:30906000-30908600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:30906200-30908600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:30906200-30908600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:30906200-30908800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr12:30906400-30908600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:30906600-30908200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:30906600-30908400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr12:30906600-30908600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:30906600-30908600	Active TSS	Fetal Muscle Trunk	muscle
13	chr12:30906800-30908000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:30906800-30908400	Active TSS	NHDF-Ad	bronchial
15	chr12:30906800-30908600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:30906800-30908600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:30906800-30908600	Active TSS	Aorta	Aorta
18	chr12:30906800-30908600	Active TSS	Fetal Brain Female	brain
19	chr12:30906800-30908600	Active TSS	Right Ventricle	heart
20	chr12:30906800-30908600	Active TSS	HSMM	muscle
21	chr12:30906800-30908800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr12:30906800-30908800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr12:30906800-30908800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:30906800-30909000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:30907000-30908200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:30907000-30908200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:30907000-30908200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:30907000-30908200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr12:30907000-30908200	Active TSS	Brain Cingulate Gyrus	brain
30	chr12:30907000-30908200	Active TSS	Brain Substantia Nigra	brain
31	chr12:30907000-30908200	Active TSS	Fetal Kidney	kidney
32	chr12:30907000-30908200	Active TSS	Rectal Smooth Muscle	rectum
33	chr12:30907000-30908200	Active TSS	GM12878-XiMat	blood
34	chr12:30907000-30908200	Active TSS	NH-A	brain
35	chr12:30907000-30908400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:30907000-30908400	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr12:30907000-30908400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:30907000-30908400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:30907000-30908400	Active TSS	Brain Hippocampus Middle	brain
40	chr12:30907000-30908400	Active TSS	Gastric	stomach
41	chr12:30907000-30908400	Active TSS	Ovary	ovary
42	chr12:30907000-30908400	Active TSS	A549	lung
43	chr12:30907000-30908600	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:30907000-30908600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:30907000-30908600	Active TSS	Brain Angular Gyrus	brain
46	chr12:30907000-30908600	Active TSS	Colonic Mucosa	Colon
47	chr12:30907000-30908600	Active TSS	Esophagus	oesophagus
48	chr12:30907000-30908600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr12:30907000-30908600	Active TSS	Fetal Stomach	stomach
50	chr12:30907000-30908600	Active TSS	Psoas Muscle	Psoas

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