Variant report

Variant	rs12034421
Chromosome Location	chr1:85528006-85528007
allele	A/C
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	EBF1	chr1:85527826-85528201	GM12878	blood:	n/a	n/a
2	MYC	chr1:85527850-85528379	MCF10A-Er-Src	breast:	n/a	n/a
3	ELK1	chr1:85527819-85528152	GM12878	blood:	n/a	n/a
4	CHD2	chr1:85527756-85528097	K562	blood:	n/a	n/a
5	NFYA	chr1:85527628-85528133	GM12878	blood:	n/a	chr1:85527902-85527912 chr1:85527900-85527915 chr1:85527900-85527918 chr1:85527900-85527915 chr1:85527900-85527914 chr1:85527900-85527913
6	PBX3	chr1:85527687-85528169	A549	lung:	n/a	chr1:85527968-85527977
7	MXI1	chr1:85527844-85528132	K562	blood:	n/a	n/a
8	PBX3	chr1:85527659-85528275	SK-N-SH	brain:	n/a	chr1:85527968-85527977
9	PBX3	chr1:85527576-85528298	SK-N-SH	brain:	n/a	chr1:85527968-85527977
10	RUNX3	chr1:85527671-85528275	GM12878	blood:	n/a	n/a
11	SP2	chr1:85527681-85528090	K562	blood:	n/a	n/a
12	FOS	chr1:85527827-85528018	MCF10A-Er-Src	breast:	n/a	chr1:85527885-85527894
13	SP1	chr1:85527665-85528161	GM12878	blood:	n/a	chr1:85527901-85527922
14	POLR2A	chr1:85527723-85528162	HCT-116	colon:	n/a	n/a
15	MAZ	chr1:85527597-85528039	GM12878	blood:	n/a	n/a
16	SP2	chr1:85527550-85528175	H1-hESC	embryonic stem cell:	n/a	n/a
17	RFX5	chr1:85527773-85528057	K562	blood:	n/a	chr1:85527903-85527912 chr1:85528020-85528028
18	NFYB	chr1:85527339-85528403	GM12878	blood:	n/a	chr1:85527902-85527912 chr1:85527900-85527915 chr1:85527900-85527915 chr1:85527900-85527914 chr1:85527900-85527913
19	SP1	chr1:85527500-85528299	HCT-116	colon:	n/a	chr1:85527901-85527922
20	SP1	chr1:85527530-85528241	A549	lung:	n/a	chr1:85527901-85527922
21	HCFC1	chr1:85527875-85528078	K562	blood:	n/a	n/a
22	CHD2	chr1:85527590-85528136	GM12878	blood:	n/a	n/a
23	PBX3	chr1:85527743-85528231	A549	lung:	n/a	chr1:85527968-85527977
24	MAFK	chr1:85527941-85528376	H1-hESC	embryonic stem cell:	n/a	chr1:85528248-85528263
25	FOS	chr1:85527829-85528044	MCF10A-Er-Src	breast:	n/a	chr1:85527885-85527894
26	PBX3	chr1:85527812-85528106	GM12878	blood:	n/a	chr1:85527968-85527977
27	WRNIP1	chr1:85527573-85528308	GM12878	blood:	n/a	n/a
28	SIN3AK20	chr1:85527696-85528357	PANC-1	pancreas:	n/a	n/a
29	CHD2	chr1:85527705-85528160	H1-hESC	embryonic stem cell:	n/a	n/a
30	FOS	chr1:85527735-85528119	GM12878	blood:	n/a	chr1:85527885-85527894
31	SIN3AK20	chr1:85527456-85528365	PANC-1	pancreas:	n/a	n/a
32	SP1	chr1:85527717-85528222	H1-hESC	embryonic stem cell:	n/a	chr1:85527901-85527922
33	KAP1	chr1:85527437-85528606	HEK293	kidney:	n/a	n/a
34	JUND	chr1:85527776-85528050	K562	blood:	n/a	chr1:85527885-85527894
35	POLR2A	chr1:85527650-85528165	HCT-116	colon:	n/a	n/a
36	YY1	chr1:85527851-85528193	GM12878	blood:	n/a	n/a
37	SP1	chr1:85527656-85528234	A549	lung:	n/a	chr1:85527901-85527922
38	CREB1	chr1:85527523-85528198	GM12878	blood:	n/a	chr1:85527883-85527896
39	E2F4	chr1:85527752-85528020	MCF10A-Er-Src	breast:	n/a	chr1:85527902-85527911 chr1:85527886-85527895 chr1:85527884-85527893
40	CREB1	chr1:85527622-85528139	HepG2	liver:	n/a	chr1:85527883-85527896
41	SIN3AK20	chr1:85527551-85528226	H1-hESC	embryonic stem cell:	n/a	n/a
42	CREB1	chr1:85527558-85528208	H1-hESC	embryonic stem cell:	n/a	chr1:85527883-85527896
43	RFX5	chr1:85527701-85528180	GM12878	blood:	n/a	chr1:85527903-85527912 chr1:85528020-85528028
44	MXI1	chr1:85527785-85528154	H1-hESC	embryonic stem cell:	n/a	n/a
45	RFX5	chr1:85527762-85528092	HepG2	liver:	n/a	chr1:85527903-85527912 chr1:85528020-85528028
46	SP1	chr1:85527609-85528239	H1-hESC	embryonic stem cell:	n/a	chr1:85527901-85527922
47	CREB1	chr1:85527637-85528181	ECC-1	luminal epithelium:	n/a	chr1:85527883-85527896
48	CREB1	chr1:85527722-85528035	A549	lung:	n/a	chr1:85527883-85527896
49	TBP	chr1:85527773-85528018	K562	blood:	n/a	n/a
50	NFYB	chr1:85527639-85528166	K562	blood:	n/a	chr1:85527902-85527912 chr1:85527900-85527915 chr1:85527900-85527915 chr1:85527900-85527914 chr1:85527900-85527913

Variant related genes	Relation type
WDR63	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6701779	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12034421	MCOLN2	cis	Thyroid	GTEx
rs12034421	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs12034421	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs12034421	MCOLN3	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85527200-85528200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:85527200-85528400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:85527400-85528200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:85527400-85528200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:85527400-85528200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:85527400-85528200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:85527400-85528200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:85527400-85528200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:85527400-85528200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:85527400-85528200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr1:85527400-85528200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr1:85527400-85528200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
13	chr1:85527400-85528200	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr1:85527400-85528200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr1:85527400-85528200	Active TSS	Brain Cingulate Gyrus	brain
16	chr1:85527400-85528200	Active TSS	Colonic Mucosa	Colon
17	chr1:85527400-85528200	Active TSS	Duodenum Mucosa	Duodenum
18	chr1:85527400-85528200	Active TSS	Fetal Heart	heart
19	chr1:85527400-85528200	Active TSS	Fetal Intestine Large	intestine
20	chr1:85527400-85528200	Active TSS	Fetal Intestine Small	intestine
21	chr1:85527400-85528200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:85527400-85528200	Flanking Active TSS	Fetal Thymus	thymus
23	chr1:85527400-85528200	Active TSS	Rectal Smooth Muscle	rectum
24	chr1:85527400-85528200	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:85527400-85528200	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr1:85527400-85528200	Active TSS	Thymus	Thymus
27	chr1:85527400-85528200	Active TSS	NHDF-Ad	bronchial
28	chr1:85527400-85528400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:85527400-85528400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:85527400-85528400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr1:85527400-85528400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:85527400-85528400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:85527400-85528400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:85527400-85528400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:85527400-85528400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr1:85527400-85528400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
37	chr1:85527400-85528400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:85527400-85528400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr1:85527400-85528400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:85527400-85528400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr1:85527400-85528400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr1:85527400-85528400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:85527400-85528400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:85527400-85528400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:85527400-85528400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:85527400-85528400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:85527400-85528400	Active TSS	Aorta	Aorta
48	chr1:85527400-85528400	Active TSS	Brain Germinal Matrix	brain
49	chr1:85527400-85528400	Active TSS	Brain Substantia Nigra	brain
50	chr1:85527400-85528400	Active TSS	Duodenum Smooth Muscle	Duodenum

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