Variant report

Variant	rs554516694
Chromosome Location	chr12:58131156-58131157
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr12:58130925-58132029	ECC-1	luminal epithelium:	n/a	n/a
2	ELF1	chr12:58130835-58131165	K562	blood:	n/a	n/a
3	ZBTB7A	chr12:58130800-58131349	K562	blood:	n/a	n/a
4	CTBP2	chr12:58129316-58131871	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3A	chr12:58131050-58131468	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr12:58130923-58132159	A549	lung:	n/a	n/a
7	HMGN3	chr12:58130976-58131246	K562	blood:	n/a	n/a
8	MAX	chr12:58130903-58131302	K562	blood:	n/a	n/a
9	MAZ	chr12:58129580-58131361	IMR90	lung:	n/a	n/a
10	SUZ12	chr12:58130289-58132014	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr12:58130912-58131244	K562	blood:	n/a	n/a
12	CBX3	chr12:58130941-58131253	K562	blood:	n/a	n/a
13	NR2F2	chr12:58129583-58131535	K562	blood:	n/a	n/a
14	MAZ	chr12:58130877-58131491	K562	blood:	n/a	n/a
15	ELF1	chr12:58130987-58131235	K562	blood:	n/a	n/a
16	ZNF143	chr12:58131114-58131287	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr12:58131073-58132109	SK-N-SH	brain:	n/a	n/a
18	SUZ12	chr12:58130135-58132131	NT2-D1	testis:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57852621..57854513-chr12:58130296..58131944,2	K562	blood:
2	chr12:57913785..57915861-chr12:58131130..58132834,2	MCF-7	breast:
3	chr12:58121545..58122179-chr12:58130671..58131607,2	MCF-7	breast:
4	chr12:58086411..58090647-chr12:58128680..58131579,3	MCF-7	breast:
5	chr12:58016846..58018792-chr12:58129433..58131831,2	K562	blood:
6	chr12:57985447..57987407-chr12:58128480..58131325,2	MCF-7	breast:
7	chr12:58086918..58087453-chr12:58130392..58131290,2	K562	blood:
8	chr12:58014906..58016961-chr12:58128240..58131170,2	K562	blood:
9	chr12:57914398..57918240-chr12:58127433..58131340,5	K562	blood:
10	chr12:57984280..57986133-chr12:58130711..58132725,2	K562	blood:
11	chr12:58112503..58116669-chr12:58128862..58132734,4	K562	blood:
12	chr12:58117957..58120676-chr12:58129042..58131410,3	K562	blood:
13	chr12:57909973..57915898-chr12:58127755..58134567,15	K562	blood:

No data

Variant related genes	Relation type
TSPAN31	TF binding region
ENSG00000111087	Chromatin interaction
ENSG00000257342	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000135506	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers 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	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv1851618	chr12:58109302-58131947	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
7	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv3363572	chr12:58129335-58133633	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv826385	chr12:58129908-58133427	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
13	esv3408774	chr12:58130710-58133658	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58118400-58132000	Strong transcription	Primary T cells from cord blood	blood
2	chr12:58119200-58132000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:58119600-58131200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:58119600-58131400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:58119600-58132400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:58119600-58132800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:58119600-58133000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:58120000-58131400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr12:58120400-58131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:58120400-58132400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:58121400-58132800	Strong transcription	Thymus	Thymus
12	chr12:58121800-58132400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:58123000-58131400	Strong transcription	Fetal Thymus	thymus
14	chr12:58127800-58133600	Weak transcription	GM12878-XiMat	blood
15	chr12:58128000-58131600	Bivalent Enhancer	Placenta	Placenta
16	chr12:58129000-58131600	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr12:58129000-58131600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:58129000-58131600	Bivalent Enhancer	Fetal Brain Male	brain
19	chr12:58129000-58131800	Bivalent Enhancer	Fetal Stomach	stomach
20	chr12:58129000-58132200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:58129000-58132400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr12:58129000-58132800	Weak transcription	Dnd41	blood
23	chr12:58129200-58131400	Bivalent Enhancer	Brain Substantia Nigra	brain
24	chr12:58129200-58131800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
25	chr12:58129200-58132600	Weak transcription	Primary B cells from cord blood	blood
26	chr12:58129200-58132600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:58129400-58131200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
28	chr12:58129400-58131200	Bivalent Enhancer	Fetal Heart	heart
29	chr12:58129400-58131400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr12:58129400-58131400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:58129400-58131600	Genic enhancers	Spleen	Spleen
32	chr12:58129400-58132200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
33	chr12:58129400-58133000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:58129600-58131400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:58129600-58131400	Bivalent Enhancer	Colonic Mucosa	Colon
36	chr12:58129600-58131400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr12:58129600-58131800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr12:58129600-58131800	Bivalent Enhancer	Fetal Intestine Small	intestine
39	chr12:58129600-58131800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
40	chr12:58129600-58132000	Flanking Active TSS	Right Ventricle	heart
41	chr12:58129600-58132600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr12:58129600-58132600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:58129600-58132800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:58129600-58133200	Enhancers	Pancreas	Pancrea
45	chr12:58129800-58131200	Bivalent Enhancer	Colon Smooth Muscle	Colon
46	chr12:58129800-58132200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:58129800-58133000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr12:58130200-58131200	Bivalent Enhancer	Stomach Mucosa	stomach
49	chr12:58130200-58131200	Flanking Bivalent TSS/Enh	HepG2	liver
50	chr12:58130200-58131400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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