Variant report

Variant	rs540889046
Chromosome Location	chr12:104681372-104681373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:185)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:185 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr12:104680529-104681560	K562	blood:	n/a	chr12:104680728-104680743 chr12:104680958-104680967
2	ATF3	chr12:104679614-104681829	A549	lung:	n/a	n/a
3	TCF7L2	chr12:104680113-104681643	PANC-1	pancreas:	n/a	n/a
4	ZBTB33	chr12:104679652-104681480	A549	lung:	n/a	n/a
5	POLR2A	chr12:104679566-104684466	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr12:104680676-104684470	A549	lung:	n/a	n/a
7	POLR2A	chr12:104680326-104681660	K562	blood:	n/a	n/a
8	POLR2A	chr12:104680500-104681704	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr12:104679817-104683502	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:104680559-104681686	HL-60	blood:	n/a	n/a
11	POLR2A	chr12:104680352-104681704	K562	blood:	n/a	n/a
12	POLR2A	chr12:104679670-104683975	HUVEC	blood vessel:	n/a	n/a
13	MAX	chr12:104680328-104681519	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3AK20	chr12:104680510-104681423	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr12:104679758-104681662	Hela-S3	cervix:	n/a	chr12:104680677-104680692
16	SP1	chr12:104679158-104684055	A549	lung:	n/a	chr12:104682628-104682639 chr12:104683086-104683100
17	MXI1	chr12:104680278-104681605	GM12878	blood:	n/a	chr12:104680677-104680692
18	POLR2A	chr12:104679672-104683881	HepG2	liver:	n/a	n/a
19	POLR2A	chr12:104681342-104681617	ECC-1	luminal epithelium:	n/a	n/a
20	STAT5A	chr12:104680564-104681438	GM12878	blood:	n/a	chr12:104681325-104681333
21	POLR2A	chr12:104681310-104681667	A549	lung:	n/a	n/a
22	MAFK	chr12:104679655-104681592	Hela-S3	cervix:	n/a	n/a
23	MAX	chr12:104680463-104681663	SK-N-SH	brain:	n/a	n/a
24	BHLHE40	chr12:104679657-104681600	K562	blood:	n/a	n/a
25	USF1	chr12:104679686-104681824	A549	lung:	n/a	chr12:104680464-104680475
26	NFYB	chr12:104680151-104681534	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:104680342-104681676	Raji	blood:	n/a	n/a
28	BACH1	chr12:104680350-104681610	H1-hESC	embryonic stem cell:	n/a	n/a
29	E2F6	chr12:104680419-104681659	H1-hESC	embryonic stem cell:	n/a	chr12:104680728-104680743 chr12:104680958-104680967
30	PBX3	chr12:104680391-104681375	SK-N-SH	brain:	n/a	chr12:104681269-104681278
31	MAX	chr12:104680285-104681402	MCF-7	breast:	n/a	n/a
32	REST	chr12:104681356-104681522	PANC-1	pancreas:	n/a	n/a
33	E2F4	chr12:104680544-104681543	MCF10A-Er-Src	breast:	n/a	chr12:104680728-104680743 chr12:104680958-104680967
34	POLR2A	chr12:104680413-104681525	GM15510	blood:	n/a	n/a
35	POLR2A	chr12:104681337-104681636	A549	lung:	n/a	n/a
36	ELF1	chr12:104680023-104681693	A549	lung:	n/a	n/a
37	POLR2A	chr12:104680220-104681825	U87	brain:	n/a	n/a
38	POLR2A	chr12:104680640-104681641	K562	blood:	n/a	n/a
39	POLR2A	chr12:104679581-104681795	IMR90	lung:	n/a	n/a
40	POLR2A	chr12:104680377-104681680	PBDE	blood:	n/a	n/a
41	POLR2A	chr12:104679831-104683884	Hela-S3	cervix:	n/a	n/a
42	TAF1	chr12:104680491-104681507	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr12:104680511-104681692	HUVEC	blood vessel:	n/a	n/a
44	TBL1XR1	chr12:104680374-104681555	GM12878	blood:	n/a	n/a
45	POLR2A	chr12:104680061-104681859	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr12:104680395-104681628	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:104680251-104683962	PANC-1	pancreas:	n/a	n/a
48	E2F6	chr12:104679566-104681843	A549	lung:	n/a	chr12:104680728-104680743 chr12:104680958-104680967
49	TAF1	chr12:104681307-104681554	Hela-S3	cervix:	n/a	n/a
50	MAX	chr12:104679656-104681671	Hela-S3	cervix:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104359459..104362433-chr12:104679529..104682592,4	K562	blood:
2	chr12:104680883..104682793-chr4:2937932..2939461,2	MCF-7	breast:
3	chr12:104530514..104533012-chr12:104679009..104681675,2	K562	blood:
4	chr12:104348328..104351209-chr12:104680724..104683661,2	K562	blood:
5	chr12:104680142..104683904-chr12:104694272..104698636,5	MCF-7	breast:
6	chr12:104234723..104236733-chr12:104679840..104682489,2	K562	blood:
7	chr12:104678772..104682731-chr12:105498551..105503490,6	K562	blood:
8	chr12:104529986..104533486-chr12:104678703..104682517,5	MCF-7	breast:
9	chr1:21112911..21113748-chr12:104680547..104681492,2	Hela-S3	cervix:
10	chr12:104681104..104682731-chr12:105500276..105502937,2	K562	blood:
11	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
12	chr12:104606650..104611349-chr12:104679680..104683932,8	K562	blood:
13	chr12:104643850..104647465-chr12:104679926..104684172,5	K562	blood:
14	chr12:104530429..104534144-chr12:104679811..104684673,6	MCF-7	breast:
15	chr12:104673431..104677021-chr12:104679201..104682284,5	MCF-7	breast:
16	chr12:104643349..104645898-chr12:104680595..104683102,2	K562	blood:
17	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:
18	chr12:104233800..104236223-chr12:104679514..104682489,2	K562	blood:
19	chr12:104530782..104534411-chr12:104679881..104682289,3	K562	blood:
20	chr12:104680695..104681479-chr9:32552140..32552648,2	NB4	blood:

No data

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000257732	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000255150	Chromatin interaction
ENSG00000127483	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000235453	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000197579	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000249673	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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv819204	chr12:104680805-104682278	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 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	chr12:104680000-104683200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:104680000-104683400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr12:104680000-104683600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:104680000-104683800	Active TSS	Aorta	Aorta
5	chr12:104680200-104682000	Active TSS	A549	lung
6	chr12:104680200-104682600	Active TSS	Brain Germinal Matrix	brain
7	chr12:104680200-104683200	Active TSS	Brain Substantia Nigra	brain
8	chr12:104680400-104681600	Active TSS	Fetal Muscle Trunk	muscle
9	chr12:104680400-104681600	Active TSS	Spleen	Spleen
10	chr12:104680400-104682000	Active TSS	Thymus	Thymus
11	chr12:104680400-104682200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:104680400-104683000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:104680400-104683000	Active TSS	Brain Angular Gyrus	brain
14	chr12:104680400-104683000	Active TSS	Fetal Brain Male	brain
15	chr12:104680400-104683200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:104680400-104683200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:104680400-104683200	Active TSS	Colon Smooth Muscle	Colon
18	chr12:104680400-104683200	Active TSS	Fetal Brain Female	brain
19	chr12:104680400-104683400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:104680400-104683400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:104680400-104683600	Active TSS	Brain Anterior Caudate	brain
22	chr12:104680400-104683600	Active TSS	Brain Cingulate Gyrus	brain
23	chr12:104680400-104683600	Active TSS	Brain Hippocampus Middle	brain
24	chr12:104680400-104683600	Active TSS	Fetal Kidney	kidney
25	chr12:104680400-104683600	Active TSS	Left Ventricle	heart
26	chr12:104680400-104683600	Active TSS	Ovary	ovary
27	chr12:104680400-104683600	Active TSS	Psoas Muscle	Psoas
28	chr12:104680400-104683600	Active TSS	Right Ventricle	heart
29	chr12:104680400-104683800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr12:104680400-104684000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr12:104680400-104684000	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr12:104680400-104684000	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr12:104680400-104684200	Active TSS	Right Atrium	heart
34	chr12:104680600-104681400	Active TSS	Primary B cells from peripheral blood	blood
35	chr12:104680600-104681400	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr12:104680600-104681400	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr12:104680600-104681600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:104680600-104681600	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr12:104680600-104681600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr12:104680600-104682000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:104680600-104682000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:104680600-104682000	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr12:104680600-104682000	Active TSS	Liver	Liver
44	chr12:104680600-104682000	Active TSS	Duodenum Mucosa	Duodenum
45	chr12:104680600-104682000	Active TSS	Fetal Heart	heart
46	chr12:104680600-104682000	Active TSS	Fetal Intestine Small	intestine
47	chr12:104680600-104682000	Active TSS	Fetal Lung	lung
48	chr12:104680600-104682000	Active TSS	Stomach Smooth Muscle	stomach
49	chr12:104680600-104682000	Active TSS	Dnd41	blood
50	chr12:104680600-104682200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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