Variant report

Variant	rs74095725
Chromosome Location	chr1:85463462-85463463
allele	G/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	POLR2A	chr1:85459671-85465061	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:85461049-85464327	GM18951	blood:	n/a	n/a
5	POLR2A	chr1:85461494-85464994	GM12892	blood:	n/a	n/a
6	MAX	chr1:85462145-85463701	GM12878	blood:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
7	CTCF	chr1:85463400-85463550	GM12867	blood:	n/a	n/a
8	POLR2A	chr1:85461102-85464291	GM18526	blood:	n/a	n/a
9	ELF1	chr1:85462435-85463628	GM12878	blood:	n/a	chr1:85462980-85462989
10	MTA3	chr1:85460680-85464125	GM12878	blood:	n/a	n/a
11	CTBP2	chr1:85462997-85464123	H1-hESC	embryonic stem cell:	n/a	n/a
12	STAT5A	chr1:85460893-85463850	GM12878	blood:	n/a	chr1:85463447-85463455 chr1:85461389-85461400
13	POLR2A	chr1:85459807-85464317	GM12892	blood:	n/a	n/a
14	CTCF	chr1:85463360-85463510	SAEC	small airway:	n/a	n/a
15	POLR2A	chr1:85462413-85463573	GM12878	blood:	n/a	n/a
16	PAX5	chr1:85462571-85463524	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:85461608-85463709	GM15510	blood:	n/a	n/a
18	POLR2A	chr1:85459795-85464999	GM12878	blood:	n/a	n/a
19	CTCF	chr1:85463360-85463510	GM12868	blood:	n/a	n/a
20	POLR2A	chr1:85463449-85463750	GM12892	blood:	n/a	n/a
21	CTCF	chr1:85463320-85463470	GM12878	blood:	n/a	n/a
22	SIN3A	chr1:85463123-85464120	H1-hESC	embryonic stem cell:	n/a	chr1:85463135-85463148 chr1:85464028-85464039
23	POLR2A	chr1:85460981-85465011	GM19099	blood:	n/a	n/a
24	CHD2	chr1:85461067-85464026	GM12878	blood:	n/a	chr1:85462833-85462843 chr1:85462244-85462251
25	CTCF	chr1:85463320-85463470	GM12866	blood:	n/a	n/a
26	POLR2A	chr1:85461031-85464258	GM12892	blood:	n/a	n/a
27	CHD1	chr1:85459740-85463594	GM12878	blood:	n/a	chr1:85462833-85462843 chr1:85462244-85462251
28	PML	chr1:85460644-85464009	GM12878	blood:	n/a	n/a
29	RUNX3	chr1:85461083-85463825	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:85461099-85464971	GM19193	blood:	n/a	n/a
31	SUZ12	chr1:85461677-85465137	NT2-D1	testis:	n/a	n/a
32	SUZ12	chr1:85463167-85464252	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr1:85463440-85463590	GM12873	blood:	n/a	n/a
34	POLR2A	chr1:85462104-85463552	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:85463360-85463881	GM12878	blood:	n/a	n/a
36	MAX	chr1:85462324-85463632	ECC-1	luminal epithelium:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
37	BHLHE40	chr1:85462315-85463615	GM12878	blood:	n/a	chr1:85463418-85463434 chr1:85463404-85463420
38	CTCF	chr1:85463440-85463590	GM06990	blood:	n/a	n/a
39	TCF3	chr1:85462960-85463533	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:85461512-85464970	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:85459862-85464245	GM18505	blood:	n/a	n/a
42	CTCF	chr1:85463320-85463470	GM12865	blood:	n/a	n/a
43	EBF1	chr1:85462862-85463476	GM12878	blood:	n/a	chr1:85463075-85463084 chr1:85462912-85462922 chr1:85463073-85463084
44	CTCF	chr1:85463440-85463590	SK-N-SH_RA	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR63-1	chr1:85463140-85463597	XLOC_000274

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

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11800303	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11807839	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11808352	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56254105	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56973472	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57386218	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59019108	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60296374	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6657216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095734	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095735	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095737	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095739	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7545349	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7546496	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7551619	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][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:119 , 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	chr1:85461600-85464400	Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr1:85461800-85463600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:85461800-85464400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:85461800-85464600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:85462000-85464200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
7	chr1:85462000-85464400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:85462000-85464400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
9	chr1:85462000-85464600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:85462200-85463600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
11	chr1:85462200-85463600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
12	chr1:85462200-85464000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:85462200-85464200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr1:85462200-85464200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:85462200-85464200	Active TSS	Aorta	Aorta
16	chr1:85462400-85463600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:85462400-85463600	Active TSS	NHDF-Ad	bronchial
18	chr1:85462400-85464200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:85462400-85464200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:85462400-85464200	Bivalent/Poised TSS	HSMM	muscle
21	chr1:85462400-85464400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
22	chr1:85462400-85464400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:85462400-85464400	Active TSS	Right Atrium	heart
24	chr1:85462600-85463600	Bivalent Enhancer	Fetal Brain Male	brain
25	chr1:85462600-85464000	Bivalent/Poised TSS	Small Intestine	intestine
26	chr1:85462600-85464200	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr1:85462600-85464200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
28	chr1:85462600-85464200	Bivalent/Poised TSS	NHLF	lung
29	chr1:85462600-85464400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:85462600-85464400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:85462600-85464400	Active TSS	Brain Angular Gyrus	brain
32	chr1:85462600-85464600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr1:85463000-85463600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr1:85463000-85463600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr1:85463000-85463600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
36	chr1:85463000-85463600	Flanking Active TSS	Lung	lung
37	chr1:85463000-85463600	Flanking Active TSS	Psoas Muscle	Psoas
38	chr1:85463000-85463600	Flanking Active TSS	Right Ventricle	heart
39	chr1:85463000-85463800	Flanking Active TSS	Pancreas	Pancrea
40	chr1:85463000-85464000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
41	chr1:85463000-85464000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
42	chr1:85463000-85464000	Flanking Bivalent TSS/Enh	Placenta	Placenta
43	chr1:85463000-85464000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr1:85463000-85464200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:85463000-85464200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
46	chr1:85463000-85464200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
47	chr1:85463000-85464200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:85463000-85464200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
49	chr1:85463000-85464200	Flanking Bivalent TSS/Enh	HMEC	breast
50	chr1:85463000-85464400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived

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