Variant report

Variant	rs181868003
Chromosome Location	chr12:49932256-49932257
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:49931839-49933116	ECC-1	luminal epithelium:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
2	REST	chr12:49931949-49932263	A549	lung:	n/a	n/a
3	ZBTB7A	chr12:49931664-49933557	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr12:49932140-49932290	AG04449	skin:	n/a	chr12:49932205-49932218
5	EGR1	chr12:49932014-49932306	K562	blood:	n/a	n/a
6	ZBTB7A	chr12:49931715-49933141	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr12:49931520-49933106	A549	lung:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
8	RCOR1	chr12:49932009-49932313	K562	blood:	n/a	n/a
9	CTBP2	chr12:49931693-49932263	H1-hESC	embryonic stem cell:	n/a	n/a
10	BCL3	chr12:49931825-49932343	A549	lung:	n/a	chr12:49931882-49931895 chr12:49932310-49932319 chr12:49931878-49931891

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49932216-49932266	HCT-116	colon:	n/a
2	chr12:49932216-49932266	GM19239	blood:	n/a
3	chr12:49932216-49932266	AoSMC	blood vessel:	n/a
4	chr12:49932216-49932266	AG09309	skin:	n/a
5	chr12:49932216-49932266	AG09319	gingival:	n/a
6	chr12:49932216-49932266	SAEC	small airway:	n/a
7	chr12:49932216-49932266	HCF	heart:	n/a
8	chr12:49932216-49932266	MCF10A-Er-Src	breast:	n/a
9	chr12:49932216-49932266	CMK	blood:	n/a
10	chr12:49932216-49932266	Hela-S3	cervix:	n/a
11	chr12:49932216-49932266	ECC-1	luminal epithelium:	n/a
12	chr12:49932216-49932266	GM12878	blood:	n/a
13	chr12:49932216-49932266	HepG2	liver:	n/a
14	chr12:49932216-49932266	HMEC	breast:	n/a
15	chr12:49932216-49932266	HCM	heart:	n/a
16	chr12:49932216-49932266	Hepatocyte	liver:	n/a
17	chr12:49932216-49932266	K562	blood:	n/a
18	chr12:49932216-49932266	A549	lung:	n/a
19	chr12:49932216-49932266	SKMC	muscle:	n/a
20	chr12:49932216-49932266	PFSK-1	brain:	n/a
21	chr12:49932216-49932266	PANC-1	pancreas:	n/a
22	chr12:49932216-49932266	HRE	kidney:	n/a
23	chr12:49932216-49932266	GM06990	blood:	n/a
24	chr12:49932216-49932266	T-47D	breast:	n/a
25	chr12:49932216-49932266	HRPEpiC	eye:	n/a
26	chr12:49932216-49932266	LNCaP	prostate:	n/a
27	chr12:49932216-49932266	AG04449	skin:	fetal
28	chr12:49932216-49932266	NHDF-neo	bronchial:	n/a
29	chr12:49932216-49932266	Jurkat	blood:	n/a
30	chr12:49932216-49932266	HUVEC	blood vessel:	n/a
31	chr12:49932216-49932266	NH-A	brain:	n/a
32	chr12:49932216-49932266	GM12891	blood:	n/a
33	chr12:49932216-49932266	NB4	blood:	n/a
34	chr12:49932216-49932266	U87	brain:	n/a
35	chr12:49932216-49932266	NT2-D1	testis:	n/a
36	chr12:49932216-49932266	RPTEC	kidney:	n/a
37	chr12:49932216-49932266	MCF-7	breast:	n/a
38	chr12:49932216-49932266	HNPCEpiC	eye:	n/a
39	chr12:49932216-49932266	HL-60	blood:	n/a
40	chr12:49932216-49932266	HCPEpiC	choroid plexus:	n/a
41	chr12:49932216-49932266	HEEpiC	esophagus:	n/a
42	chr12:49932216-49932266	GM12892	blood:	n/a
43	chr12:49932216-49932266	NHBE	bronchial:	n/a
44	chr12:49932216-49932266	AG04450	lung:	fetal
45	chr12:49932216-49932266	AG10803	skin:	n/a
46	chr12:49932216-49932266	HRCEpiC	kidney:	n/a
47	chr12:49932216-49932266	BE2_C	brain:	n/a
48	chr12:49932216-49932266	IMR90	lung:	fetal
49	chr12:49932216-49932266	SK-N-SH_RA	brain:	n/a
50	chr12:49932216-49932266	SK-N-SH	brain:	n/a

(count:7 , 50 per page) page: 1

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:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNH3-2	chr12:49932202-49932791	NONHSAT028109

No data

Variant related genes	Relation type
KCNH3	TF binding region
KCNH3	CpG island
ENSG00000258101	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000187778	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:119 , 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	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
3	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
4	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
5	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
6	chr12:49931200-49932400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
10	chr12:49931200-49932400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
11	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
12	chr12:49931200-49932400	Flanking Active TSS	Right Ventricle	heart
13	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
14	chr12:49931200-49932800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr12:49931200-49932800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:49931200-49932800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:49931200-49933400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr12:49931200-49933400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:49931200-49935000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr12:49931400-49932400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr12:49931400-49932400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
28	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:49931400-49932400	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
31	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
32	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
33	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
34	chr12:49931400-49932400	Flanking Active TSS	Pancreas	Pancrea
35	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
36	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
37	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
38	chr12:49931400-49932400	Flanking Active TSS	Spleen	Spleen
39	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
40	chr12:49931400-49932400	Flanking Bivalent TSS/Enh	NHEK	skin
41	chr12:49931400-49932600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:49931400-49933000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:49931400-49933000	Active TSS	Aorta	Aorta
44	chr12:49931400-49933200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:49931400-49933200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr12:49931400-49933400	Active TSS	Right Atrium	heart
47	chr12:49931600-49932400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr12:49931600-49932400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:49931600-49932400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:49931600-49932400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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