Variant report

Variant	rs920340
Chromosome Location	chr1:85462750-85462751
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	ZEB1	chr1:85462507-85463768	GM12878	blood:	n/a	n/a
2	EBF1	chr1:85461040-85464248	GM12878	blood:	n/a	chr1:85463075-85463084 chr1:85462912-85462922 chr1:85463073-85463084
3	USF2	chr1:85462149-85462959	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:85462551-85462810	GM12891	blood:	n/a	n/a
5	SIN3AK20	chr1:85462371-85463242	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:85459671-85465061	GM12892	blood:	n/a	n/a
7	TBP	chr1:85461053-85462869	GM12878	blood:	n/a	n/a
8	E2F6	chr1:85462424-85463020	H1-hESC	embryonic stem cell:	n/a	chr1:85462835-85462844 chr1:85462827-85462839 chr1:85462983-85462992
9	MYC	chr1:85462642-85462929	MCF-7	breast:	n/a	chr1:85462813-85462822
10	TBP	chr1:85462200-85462852	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:85461049-85464327	GM18951	blood:	n/a	n/a
12	MAX	chr1:85462596-85462838	K562	blood:	n/a	chr1:85462813-85462822
13	SIN3AK20	chr1:85462438-85462852	PANC-1	pancreas:	n/a	n/a
14	MAX	chr1:85462304-85463390	H1-hESC	embryonic stem cell:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
15	POLR2A	chr1:85461494-85464994	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:85462153-85462824	PANC-1	pancreas:	n/a	n/a
17	E2F6	chr1:85462631-85462829	K562	blood:	n/a	n/a
18	TAF1	chr1:85462587-85462817	GM12878	blood:	n/a	n/a
19	MAX	chr1:85462145-85463701	GM12878	blood:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
20	RELA	chr1:85461100-85462794	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:85462562-85462852	Gliobla	brain:	n/a	n/a
22	ZNF143	chr1:85462642-85463259	GM12878	blood:	n/a	chr1:85463074-85463092 chr1:85463202-85463220 chr1:85462987-85463005
23	RELA	chr1:85461015-85462796	GM18505	blood:	n/a	n/a
24	POLR2A	chr1:85462639-85462848	A549	lung:	n/a	n/a
25	POLR2A	chr1:85461102-85464291	GM18526	blood:	n/a	n/a
26	ELF1	chr1:85462435-85463628	GM12878	blood:	n/a	chr1:85462980-85462989
27	ZBTB7A	chr1:85462564-85463389	ECC-1	luminal epithelium:	n/a	chr1:85463071-85463079
28	MTA3	chr1:85460680-85464125	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:85462588-85462813	ECC-1	luminal epithelium:	n/a	n/a
30	USF1	chr1:85462253-85462969	H1-hESC	embryonic stem cell:	n/a	n/a
31	TCF3	chr1:85462514-85462948	GM12878	blood:	n/a	n/a
32	STAT5A	chr1:85460893-85463850	GM12878	blood:	n/a	chr1:85463447-85463455 chr1:85461389-85461400
33	POLR2A	chr1:85459807-85464317	GM12892	blood:	n/a	n/a
34	MXI1	chr1:85462421-85462838	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:85462665-85462819	A549	lung:	n/a	n/a
36	POLR2A	chr1:85462413-85463573	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:85462550-85462818	H1-hESC	embryonic stem cell:	n/a	n/a
38	RELA	chr1:85461141-85463082	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:85462524-85462829	HCT-116	colon:	n/a	n/a
40	BACH1	chr1:85462556-85462963	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr1:85462319-85463395	A549	lung:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
42	CHD1	chr1:85462604-85462804	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr1:85462559-85463420	MCF-7	breast:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
44	HA-E2F1	chr1:85462153-85462827	MCF-7	breast:	n/a	chr1:85462244-85462251
45	POLR2A	chr1:85462547-85462848	A549	lung:	n/a	n/a
46	TAF1	chr1:85462540-85462841	GM12892	blood:	n/a	n/a
47	PAX5	chr1:85462571-85463524	GM12892	blood:	n/a	n/a
48	POLR2A	chr1:85461608-85463709	GM15510	blood:	n/a	n/a
49	RELA	chr1:85461055-85463441	GM15510	blood:	n/a	n/a
50	TAF1	chr1:85462529-85462832	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:85462700-85462750	BE2_C	brain:	n/a
2	chr1:85462700-85462750	HCT-116	colon:	n/a
3	chr1:85462700-85462750	GM12891	blood:	n/a
4	chr1:85462700-85462750	HEEpiC	esophagus:	n/a
5	chr1:85462700-85462750	NH-A	brain:	n/a
6	chr1:85462700-85462750	SK-N-MC	brain:	n/a
7	chr1:85462700-85462750	U87	brain:	n/a
8	chr1:85462700-85462750	NB4	blood:	n/a
9	chr1:85462700-85462750	MCF10A-Er-Src	breast:	n/a
10	chr1:85462700-85462750	HEK293	kidney:	embryo
11	chr1:85462700-85462750	AG04450	lung:	fetal
12	chr1:85462700-85462750	NHDF-neo	bronchial:	n/a
13	chr1:85462700-85462750	AG10803	skin:	n/a
14	chr1:85462700-85462750	GM06990	blood:	n/a
15	chr1:85462700-85462750	HCF	heart:	n/a
16	chr1:85462700-85462750	AG09319	gingival:	n/a
17	chr1:85462700-85462750	SKMC	muscle:	n/a
18	chr1:85462700-85462750	ProgFib	skin:	n/a
19	chr1:85462700-85462750	GM19239	blood:	n/a
20	chr1:85462700-85462750	NT2-D1	testis:	n/a
21	chr1:85462700-85462750	HRPEpiC	eye:	n/a
22	chr1:85462700-85462750	PrEC	prostate:	n/a
23	chr1:85462700-85462750	NHBE	bronchial:	n/a
24	chr1:85462700-85462750	Hepatocyte	liver:	n/a
25	chr1:85462700-85462750	MCF-7	breast:	n/a
26	chr1:85462700-85462750	SK-N-SH_RA	brain:	n/a
27	chr1:85462700-85462750	HL-60	blood:	n/a
28	chr1:85462700-85462750	SAEC	small airway:	n/a
29	chr1:85462700-85462750	ovcar-3	ovarian:	n/a
30	chr1:85462700-85462750	HCM	heart:	n/a
31	chr1:85462700-85462750	T-47D	breast:	n/a
32	chr1:85462700-85462750	HMEC	breast:	n/a
33	chr1:85462700-85462750	IMR90	lung:	fetal
34	chr1:85462700-85462750	ECC-1	luminal epithelium:	n/a
35	chr1:85462700-85462750	HIPEpiC	eye:	n/a
36	chr1:85462700-85462750	GM12878	blood:	n/a
37	chr1:85462700-85462750	PANC-1	pancreas:	n/a
38	chr1:85462700-85462750	LNCaP	prostate:	n/a
39	chr1:85462700-85462750	PFSK-1	brain:	n/a
40	chr1:85462700-85462750	GM12892	blood:	n/a
41	chr1:85462700-85462750	HAEpiC	amniotic membrane:	n/a
42	chr1:85462700-85462750	AoSMC	blood vessel:	n/a
43	chr1:85462700-85462750	RPTEC	kidney:	n/a
44	chr1:85462700-85462750	Caco-2	colon:	n/a
45	chr1:85462700-85462750	HepG2	liver:	n/a
46	chr1:85462700-85462750	HRE	kidney:	n/a
47	chr1:85462700-85462750	HPAEpiC	pulmonary alveolar:	n/a
48	chr1:85462700-85462750	HNPCEpiC	eye:	n/a
49	chr1:85462700-85462750	Hela-S3	cervix:	n/a
50	chr1:85462700-85462750	AG04449	skin:	fetal

Variant related genes	Relation type
MCOLN2	TF binding region
WDR63	TF binding region
MCOLN2	CpG island
WDR63	CpG island

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10782535	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873675	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458401	1.00[ASN][1000 genomes]
rs2039814	1.00[ASN][1000 genomes]
rs486647	1.00[ASN][1000 genomes]
rs4907122	1.00[ASN][1000 genomes]
rs496561	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs499579	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs511765	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs517156	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs531169	1.00[ASN][1000 genomes]
rs534908	1.00[ASN][1000 genomes]
rs562126	1.00[ASN][1000 genomes]
rs586403	1.00[ASN][1000 genomes]
rs589227	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs599137	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs599888	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs607298	1.00[ASN][1000 genomes]
rs614194	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61769365	1.00[ASN][1000 genomes]
rs641427	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6576737	1.00[ASN][1000 genomes]
rs6576740	1.00[ASN][1000 genomes]
rs6576742	1.00[ASN][1000 genomes]
rs6576743	1.00[ASN][1000 genomes]
rs664763	1.00[ASN][1000 genomes]
rs6684210	1.00[ASN][1000 genomes]
rs6692907	0.83[AFR][1000 genomes]
rs679932	1.00[ASN][1000 genomes]
rs680330	1.00[ASN][1000 genomes]
rs7519717	1.00[ASN][1000 genomes]
rs7533496	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537692	1.00[ASN][1000 genomes]
rs9804097	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	esv3515392	chr1:85437980-85465392	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3515393	chr1:85437980-85465392	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	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
9	esv3410983	chr1:85461789-85464337	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85460400-85463800	Active TSS	GM12878-XiMat	blood
2	chr1:85461200-85463400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr1:85461600-85464400	Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr1:85461800-85462800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:85461800-85463200	Active TSS	Rectal Smooth Muscle	rectum
6	chr1:85461800-85463200	Active TSS	A549	lung
7	chr1:85461800-85463600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:85461800-85464400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:85461800-85464600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:85462000-85463000	Active TSS	Colonic Mucosa	Colon
11	chr1:85462000-85463000	Active TSS	Right Ventricle	heart
12	chr1:85462000-85464200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
13	chr1:85462000-85464400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:85462000-85464400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr1:85462000-85464600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr1:85462200-85462800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr1:85462200-85462800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
18	chr1:85462200-85462800	Flanking Active TSS	Liver	Liver
19	chr1:85462200-85462800	Flanking Bivalent TSS/Enh	Placenta	Placenta
20	chr1:85462200-85462800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
21	chr1:85462200-85462800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr1:85462200-85463000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:85462200-85463000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:85462200-85463000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:85462200-85463000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:85462200-85463000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:85462200-85463000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:85462200-85463000	Active TSS	Lung	lung
29	chr1:85462200-85463000	Active TSS	Ovary	ovary
30	chr1:85462200-85463000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
31	chr1:85462200-85463000	Active TSS	HMEC	breast
32	chr1:85462200-85463200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:85462200-85463200	Bivalent/Poised TSS	NH-A	brain
34	chr1:85462200-85463400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:85462200-85463400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr1:85462200-85463600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr1:85462200-85463600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
38	chr1:85462200-85464000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:85462200-85464200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr1:85462200-85464200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:85462200-85464200	Active TSS	Aorta	Aorta
42	chr1:85462400-85462800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:85462400-85462800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:85462400-85462800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
45	chr1:85462400-85462800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
46	chr1:85462400-85462800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
47	chr1:85462400-85462800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
48	chr1:85462400-85462800	Bivalent/Poised TSS	HepG2	liver
49	chr1:85462400-85462800	Flanking Bivalent TSS/Enh	Osteobl	bone
50	chr1:85462400-85463000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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