Variant report

Variant	rs529084038
Chromosome Location	chr12:49932624-49932625
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	MAX	chr12:49932500-49932954	A549	lung:	n/a	chr12:49932763-49932772
2	YY1	chr12:49932616-49932825	HCT-116	colon:	n/a	chr12:49932678-49932687 chr12:49932786-49932800 chr12:49932675-49932684 chr12:49932786-49932795 chr12:49932739-49932753
3	MAX	chr12:49932459-49933072	K562	blood:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
4	YY1	chr12:49932590-49933055	GM12892	blood:	n/a	chr12:49932940-49932954 chr12:49932678-49932687 chr12:49932938-49932949 chr12:49932786-49932800 chr12:49932675-49932684 chr12:49932940-49932949 chr12:49932786-49932795 chr12:49932739-49932753
5	POLR2A	chr12:49932550-49933012	HCT-116	colon:	n/a	n/a
6	MAX	chr12:49931839-49933116	ECC-1	luminal epithelium:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
7	MAZ	chr12:49932611-49932805	Hela-S3	cervix:	n/a	chr12:49932763-49932772
8	MAZ	chr12:49932492-49933675	IMR90	lung:	n/a	chr12:49932763-49932772
9	EGR1	chr12:49932546-49932743	GM12878	blood:	n/a	chr12:49932677-49932686 chr12:49932673-49932687 chr12:49932676-49932689 chr12:49932676-49932689 chr12:49932675-49932689 chr12:49932676-49932686 chr12:49932676-49932689
10	ZBTB7A	chr12:49931664-49933557	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr12:49932300-49932878	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr12:49932559-49932843	H1-neurons	neurons:	n/a	n/a
13	EGR1	chr12:49932529-49932859	K562	blood:	n/a	chr12:49932677-49932686 chr12:49932673-49932687 chr12:49932676-49932689 chr12:49932676-49932689 chr12:49932675-49932689 chr12:49932676-49932686 chr12:49932676-49932689
14	ZBTB7A	chr12:49931715-49933141	ECC-1	luminal epithelium:	n/a	n/a
15	MAX	chr12:49931520-49933106	A549	lung:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
16	EGR1	chr12:49932474-49932842	K562	blood:	n/a	chr12:49932677-49932686 chr12:49932673-49932687 chr12:49932676-49932689 chr12:49932676-49932689 chr12:49932675-49932689 chr12:49932676-49932686 chr12:49932676-49932689
17	MAZ	chr12:49932487-49932991	K562	blood:	n/a	chr12:49932763-49932772
18	MAZ	chr12:49932273-49932886	GM12878	blood:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
19	TCF12	chr12:49932431-49933000	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr12:49932541-49933056	HUVEC	blood vessel:	n/a	n/a
21	ZBTB7A	chr12:49932492-49932703	K562	blood:	n/a	n/a

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	chr12:49932202-49932791	NONHSAT028109

Variant related genes	Relation type
KCNH3	TF binding region
ENSG00000187778	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000167553	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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49931200-49932800	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr12:49931200-49932800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:49931200-49932800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:49931200-49933400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr12:49931200-49933400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:49931200-49935000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:49931400-49933000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:49931400-49933000	Active TSS	Aorta	Aorta
9	chr12:49931400-49933200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:49931400-49933200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:49931400-49933400	Active TSS	Right Atrium	heart
12	chr12:49931600-49932800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
13	chr12:49931600-49933000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:49931600-49933000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr12:49931600-49933000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr12:49931600-49933000	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
17	chr12:49931600-49933200	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr12:49931600-49933800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr12:49931800-49934200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr12:49932000-49932800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
21	chr12:49932000-49932800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr12:49932000-49932800	Flanking Bivalent TSS/Enh	Placenta	Placenta
23	chr12:49932000-49932800	Flanking Bivalent TSS/Enh	Dnd41	blood
24	chr12:49932200-49932800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:49932200-49932800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:49932200-49932800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:49932200-49932800	Enhancers	Liver	Liver
28	chr12:49932200-49932800	Active TSS	Brain Substantia Nigra	brain
29	chr12:49932200-49932800	Bivalent Enhancer	Fetal Brain Male	brain
30	chr12:49932200-49932800	Active TSS	Ovary	ovary
31	chr12:49932200-49932800	Bivalent/Poised TSS	Thymus	Thymus
32	chr12:49932200-49933000	Active TSS	Hela-S3	cervix
33	chr12:49932200-49933000	Bivalent/Poised TSS	HSMM	muscle
34	chr12:49932200-49933200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr12:49932200-49933200	Bivalent/Poised TSS	Psoas Muscle	Psoas
36	chr12:49932200-49933200	Bivalent/Poised TSS	NHLF	lung
37	chr12:49932200-49933400	Active TSS	Gastric	stomach
38	chr12:49932200-49933600	Active TSS	Brain Angular Gyrus	brain
39	chr12:49932200-49933600	Active TSS	A549	lung
40	chr12:49932400-49932800	Bivalent/Poised TSS	Primary B cells from peripheral blood	blood
41	chr12:49932400-49932800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:49932400-49932800	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:49932400-49932800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
44	chr12:49932400-49932800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
45	chr12:49932400-49932800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
46	chr12:49932400-49932800	Bivalent/Poised TSS	Fetal Stomach	stomach
47	chr12:49932400-49932800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
48	chr12:49932400-49932800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
49	chr12:49932400-49932800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr12:49932400-49933000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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