Variant report

Variant	rs11046106
Chromosome Location	chr12:21680478-21680479
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	RAD21	chr12:21680422-21681108	H1-hESC	embryonic stem cell:	n/a	chr12:21680886-21680900 chr12:21680865-21680878
2	POLR2A	chr12:21680356-21681169	ECC-1	luminal epithelium:	n/a	n/a
3	TAF1	chr12:21680321-21681122	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:21680323-21681092	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr12:21680335-21681218	A549	lung:	n/a	n/a
6	POLR2A	chr12:21680359-21681086	A549	lung:	n/a	n/a
7	CTBP2	chr12:21680322-21681135	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF143	chr12:21680402-21681050	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr12:21680469-21681074	H1-hESC	embryonic stem cell:	n/a	chr12:21680971-21680980
10	POLR2A	chr12:21680401-21681133	A549	lung:	n/a	n/a
11	CREB1	chr12:21680383-21681134	A549	lung:	n/a	n/a
12	POLR2A	chr12:21680312-21680953	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZBTB7A	chr12:21680151-21681210	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr12:21680401-21681209	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr12:21680452-21681194	GM18951	blood:	n/a	n/a
16	TCF12	chr12:21680317-21681217	A549	lung:	n/a	n/a
17	RAD21	chr12:21680467-21681115	H1-hESC	embryonic stem cell:	n/a	chr12:21680886-21680900 chr12:21680865-21680878
18	TBP	chr12:21680357-21681147	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:21680153-21681244	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZBTB7A	chr12:21680082-21680979	ECC-1	luminal epithelium:	n/a	n/a
21	TCF12	chr12:21680335-21681193	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr12:21680273-21681302	A549	lung:	n/a	n/a

Variant related genes	Relation type
C12orf39	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv557743	chr12:21670410-21688900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv898897	chr12:21680363-21781141	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11046106	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs11046106	GOLT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21679800-21681200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:21679800-21681400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr12:21679800-21681400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:21679800-21681600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:21680000-21680600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
6	chr12:21680000-21680600	Bivalent Enhancer	Stomach Mucosa	stomach
7	chr12:21680000-21680800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:21680000-21680800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
9	chr12:21680000-21681000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr12:21680000-21681000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:21680000-21681000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:21680000-21681200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:21680000-21681200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:21680000-21681200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:21680000-21681200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:21680000-21681200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:21680000-21681200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:21680000-21681200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:21680000-21681200	Active TSS	Brain Angular Gyrus	brain
20	chr12:21680000-21681200	Active TSS	Brain Substantia Nigra	brain
21	chr12:21680000-21681200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
22	chr12:21680000-21681200	Active TSS	Psoas Muscle	Psoas
23	chr12:21680000-21681200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
24	chr12:21680000-21681200	Active TSS	Stomach Smooth Muscle	stomach
25	chr12:21680000-21681200	Bivalent/Poised TSS	GM12878-XiMat	blood
26	chr12:21680000-21681400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:21680000-21681400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:21680000-21681400	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr12:21680000-21681400	Flanking Active TSS	Liver	Liver
30	chr12:21680000-21681400	Active TSS	Brain Anterior Caudate	brain
31	chr12:21680000-21681400	Active TSS	Brain Cingulate Gyrus	brain
32	chr12:21680000-21681400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr12:21680000-21681400	Active TSS	Right Ventricle	heart
34	chr12:21680000-21681400	Bivalent/Poised TSS	NHDF-Ad	bronchial
35	chr12:21680200-21680600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
36	chr12:21680200-21680600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:21680200-21680600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:21680200-21680600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
39	chr12:21680200-21680600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr12:21680200-21680600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
41	chr12:21680200-21680800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
42	chr12:21680200-21680800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
43	chr12:21680200-21680800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr12:21680200-21680800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:21680200-21680800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:21680200-21680800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
47	chr12:21680200-21680800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
48	chr12:21680200-21681000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:21680200-21681000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:21680200-21681000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle

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