Variant report

Variant	rs4907128
Chromosome Location	chr1:85527974-85527975
allele	A/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	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	SP2	chr1:85527843-85527991	K562	blood:	n/a	n/a
44	RFX5	chr1:85527701-85528180	GM12878	blood:	n/a	chr1:85527903-85527912 chr1:85528020-85528028
45	MXI1	chr1:85527785-85528154	H1-hESC	embryonic stem cell:	n/a	n/a
46	RFX5	chr1:85527762-85528092	HepG2	liver:	n/a	chr1:85527903-85527912 chr1:85528020-85528028
47	SP1	chr1:85527609-85528239	H1-hESC	embryonic stem cell:	n/a	chr1:85527901-85527922
48	CREB1	chr1:85527637-85528181	ECC-1	luminal epithelium:	n/a	chr1:85527883-85527896
49	CREB1	chr1:85527722-85528035	A549	lung:	n/a	chr1:85527883-85527896
50	TBP	chr1:85527773-85528018	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:85527943-85527993	NHDF-neo	bronchial:	n/a
2	chr1:85527943-85527993	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:85527943-85527993	GM12878	blood:	n/a
4	chr1:85527943-85527993	HCT-116	colon:	n/a
5	chr1:85527943-85527993	HCF	heart:	n/a
6	chr1:85527943-85527993	SK-N-SH	brain:	n/a
7	chr1:85527943-85527993	SKMC	muscle:	n/a
8	chr1:85527943-85527993	HIPEpiC	eye:	n/a
9	chr1:85527943-85527993	IMR90	lung:	fetal
10	chr1:85527943-85527993	SK-N-MC	brain:	n/a
11	chr1:85527943-85527993	AG09319	gingival:	n/a
12	chr1:85527943-85527993	CMK	blood:	n/a
13	chr1:85527943-85527993	NHBE	bronchial:	n/a
14	chr1:85527943-85527993	Jurkat	blood:	n/a
15	chr1:85527943-85527993	HAEpiC	amniotic membrane:	n/a
16	chr1:85527943-85527993	ovcar-3	ovarian:	n/a
17	chr1:85527943-85527993	AG04450	lung:	fetal
18	chr1:85527943-85527993	MCF10A-Er-Src	breast:	n/a
19	chr1:85527943-85527993	BE2_C	brain:	n/a
20	chr1:85527943-85527993	PrEC	prostate:	n/a
21	chr1:85527943-85527993	HNPCEpiC	eye:	n/a
22	chr1:85527943-85527993	Hepatocyte	liver:	n/a
23	chr1:85527943-85527993	BJ	skin:	n/a
24	chr1:85527943-85527993	HRCEpiC	kidney:	n/a
25	chr1:85527943-85527993	AG04449	skin:	fetal
26	chr1:85527943-85527993	K562	blood:	n/a
27	chr1:85527943-85527993	HEEpiC	esophagus:	n/a
28	chr1:85527943-85527993	NT2-D1	testis:	n/a
29	chr1:85527943-85527993	HCM	heart:	n/a
30	chr1:85527943-85527993	HepG2	liver:	n/a
31	chr1:85527943-85527993	HRE	kidney:	n/a
32	chr1:85527943-85527993	A549	lung:	n/a
33	chr1:85527943-85527993	ECC-1	luminal epithelium:	n/a
34	chr1:85527943-85527993	Hela-S3	cervix:	n/a
35	chr1:85527943-85527993	PANC-1	pancreas:	n/a
36	chr1:85527943-85527993	SAEC	small airway:	n/a
37	chr1:85527943-85527993	NB4	blood:	n/a
38	chr1:85527943-85527993	HUVEC	blood vessel:	n/a
39	chr1:85527943-85527993	HCPEpiC	choroid plexus:	n/a
40	chr1:85527943-85527993	GM12891	blood:	n/a
41	chr1:85527943-85527993	MCF-7	breast:	n/a
42	chr1:85527943-85527993	GM12892	blood:	n/a
43	chr1:85527943-85527993	LNCaP	prostate:	n/a
44	chr1:85527943-85527993	HRPEpiC	eye:	n/a
45	chr1:85527943-85527993	ProgFib	skin:	n/a
46	chr1:85527943-85527993	AoSMC	blood vessel:	n/a
47	chr1:85527943-85527993	GM06990	blood:	n/a
48	chr1:85527943-85527993	H1-hESC	embryonic stem cell:	embryo
49	chr1:85527943-85527993	GM19239	blood:	n/a
50	chr1:85527943-85527993	HMEC	breast:	n/a

Variant related genes	Relation type
WDR63	TF binding region
WDR63	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10782538	0.81[YRI][hapmap]
rs11161516	0.84[AFR][1000 genomes]
rs11808352	0.82[CEU][hapmap]
rs6576745	0.83[ASW][hapmap];0.92[LWK][hapmap];0.90[AFR][1000 genomes]
rs6576747	0.83[ASW][hapmap];0.94[LWK][hapmap];0.90[AFR][1000 genomes]
rs6695223	0.83[ASW][hapmap];0.94[LWK][hapmap];0.90[AFR][1000 genomes]
rs6697585	1.00[YRI][hapmap]
rs7545349	0.82[CEU][hapmap]
rs7551469	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs898035	0.90[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4907128	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs4907128	HHIP	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85527200-85528000	Active TSS	GM12878-XiMat	blood
2	chr1:85527200-85528200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:85527200-85528400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:85527400-85528000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr1:85527400-85528000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:85527400-85528000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr1:85527400-85528000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:85527400-85528000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:85527400-85528000	Active TSS	Brain Hippocampus Middle	brain
10	chr1:85527400-85528000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr1:85527400-85528000	Active TSS	NHEK	skin
12	chr1:85527400-85528200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:85527400-85528200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:85527400-85528200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:85527400-85528200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:85527400-85528200	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:85527400-85528200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:85527400-85528200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:85527400-85528200	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:85527400-85528200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr1:85527400-85528200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
22	chr1:85527400-85528200	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr1:85527400-85528200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:85527400-85528200	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:85527400-85528200	Active TSS	Colonic Mucosa	Colon
26	chr1:85527400-85528200	Active TSS	Duodenum Mucosa	Duodenum
27	chr1:85527400-85528200	Active TSS	Fetal Heart	heart
28	chr1:85527400-85528200	Active TSS	Fetal Intestine Large	intestine
29	chr1:85527400-85528200	Active TSS	Fetal Intestine Small	intestine
30	chr1:85527400-85528200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:85527400-85528200	Flanking Active TSS	Fetal Thymus	thymus
32	chr1:85527400-85528200	Active TSS	Rectal Smooth Muscle	rectum
33	chr1:85527400-85528200	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr1:85527400-85528200	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:85527400-85528200	Active TSS	Thymus	Thymus
36	chr1:85527400-85528200	Active TSS	NHDF-Ad	bronchial
37	chr1:85527400-85528400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr1:85527400-85528400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:85527400-85528400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr1:85527400-85528400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:85527400-85528400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:85527400-85528400	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:85527400-85528400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:85527400-85528400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr1:85527400-85528400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
46	chr1:85527400-85528400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:85527400-85528400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr1:85527400-85528400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:85527400-85528400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr1:85527400-85528400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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