Variant report

Variant	rs539554481
Chromosome Location	chr12:49931881-49931882
allele	C/G
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	SIN3AK20	chr12:49931814-49932067	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:49931440-49932126	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr12:49931780-49932070	GM12872	blood:	n/a	n/a
4	CTCF	chr12:49931860-49932010	HCM	heart:	n/a	n/a
5	CTCF	chr12:49931840-49931990	GM12865	blood:	n/a	n/a
6	CTCF	chr12:49931880-49932030	RPTEC	kidney:	n/a	n/a
7	MAX	chr12:49931839-49933116	ECC-1	luminal epithelium:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
8	EGR1	chr12:49931601-49931927	K562	blood:	n/a	n/a
9	CTCF	chr12:49931880-49932030	AG04449	skin:	n/a	n/a
10	RAD21	chr12:49931749-49932187	H1-hESC	embryonic stem cell:	n/a	chr12:49931861-49931874 chr12:49931997-49932007
11	CTCF	chr12:49931860-49932010	RPTEC	kidney:	n/a	n/a
12	CTCF	chr12:49931860-49932010	HRPEpiC	eye:	n/a	n/a
13	ZBTB7A	chr12:49931664-49933557	ECC-1	luminal epithelium:	n/a	n/a
14	ZBTB7A	chr12:49931632-49932170	K562	blood:	n/a	n/a
15	UBTF	chr12:49931641-49932026	K562	blood:	n/a	n/a
16	CTCF	chr12:49931860-49932010	GM12873	blood:	n/a	n/a
17	MAZ	chr12:49931828-49932060	K562	blood:	n/a	n/a
18	USF1	chr12:49931843-49932197	H1-hESC	embryonic stem cell:	n/a	chr12:49931871-49931887 chr12:49931854-49931870
19	ZBTB7A	chr12:49931715-49933141	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr12:49931520-49933106	A549	lung:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
21	CTCF	chr12:49931880-49932030	GM12868	blood:	n/a	n/a
22	SUZ12	chr12:49931448-49932210	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr12:49931860-49932010	GM12874	blood:	n/a	n/a
24	CTCF	chr12:49931800-49931950	A549	lung:	n/a	n/a
25	CTCF	chr12:49931880-49932030	WERI-Rb-1	eye:	n/a	n/a
26	MAX	chr12:49931804-49932146	K562	blood:	n/a	n/a
27	USF1	chr12:49931860-49932149	H1-hESC	embryonic stem cell:	n/a	chr12:49931871-49931887
28	CREB1	chr12:49931581-49931900	A549	lung:	n/a	n/a
29	CTCF	chr12:49931840-49931990	GM12875	blood:	n/a	n/a
30	HMGN3	chr12:49931648-49931979	K562	blood:	n/a	n/a
31	RAD21	chr12:49931879-49932059	K562	blood:	n/a	chr12:49931997-49932007
32	UBTF	chr12:49931624-49931949	K562	blood:	n/a	n/a
33	CTCF	chr12:49931840-49931990	GM12864	blood:	n/a	n/a
34	CTBP2	chr12:49931693-49932263	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr12:49931760-49931910	GM12874	blood:	n/a	n/a
36	BCL3	chr12:49931825-49932343	A549	lung:	n/a	chr12:49931882-49931895 chr12:49932310-49932319 chr12:49931878-49931891

No.	Distal block	Cell Line	Cell type
1	chr12:49930852..49937653-chr12:49953841..49959391,7	K562	blood:
2	chr12:49759022..49764027-chr12:49928293..49932911,8	MCF-7	breast:
3	chr12:49657477..49660356-chr12:49930384..49933439,3	K562	blood:
4	chr12:49759353..49761548-chr12:49931777..49934189,4	K562	blood:
5	chr12:49759353..49762276-chr12:49930939..49933731,4	K562	blood:
6	chr12:49930865..49935032-chr12:49959689..49963246,5	K562	blood:
7	chr12:49931420..49936579-chr12:49960006..49963071,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNH3-2	chr12:49931669-49931973	NONHSAT028109

Variant related genes	Relation type
KCNH3	TF binding region
ENSG00000123352	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000258101	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	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv1801776	chr12:49915354-49934565	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3431223	chr12:49931235-49934833	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49931000-49932400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
2	chr12:49931200-49932000	Bivalent Enhancer	Fetal Thymus	thymus
3	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
4	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
5	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
6	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
7	chr12:49931200-49932400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
11	chr12:49931200-49932400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
12	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
13	chr12:49931200-49932400	Flanking Active TSS	Right Ventricle	heart
14	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
15	chr12:49931200-49932800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr12:49931200-49932800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:49931200-49932800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:49931200-49933400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr12:49931200-49933400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:49931200-49935000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:49931400-49932000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:49931400-49932000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr12:49931400-49932000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
24	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
29	chr12:49931400-49932200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:49931400-49932200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
32	chr12:49931400-49932200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
33	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
34	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	Thymus	Thymus
35	chr12:49931400-49932200	Flanking Bivalent TSS/Enh	Osteobl	bone
36	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
40	chr12:49931400-49932400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr12:49931400-49932400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
44	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:49931400-49932400	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
47	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
48	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
49	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
50	chr12:49931400-49932400	Flanking Active TSS	Pancreas	Pancrea

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