Variant report

Variant	rs57638901
Chromosome Location	chr1:46835954-46835955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:46835209-46836290	K562	blood:	n/a	n/a
2	ZNF384	chr1:46835904-46836605	K562	blood:	n/a	n/a
3	NFYA	chr1:46835953-46836297	K562	blood:	n/a	n/a
4	JUND	chr1:46835598-46836176	K562	blood:	n/a	n/a
5	RCOR1	chr1:46835633-46836249	K562	blood:	n/a	n/a
6	USF1	chr1:46835870-46836353	K562	blood:	n/a	n/a
7	BHLHE40	chr1:46835870-46836329	K562	blood:	n/a	n/a
8	EP300	chr1:46835662-46836155	K562	blood:	n/a	n/a
9	ZNF384	chr1:46835950-46836391	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:46835679-46836279	K562	blood:	n/a	n/a
11	POLR2A	chr1:46833899-46836306	K562	blood:	n/a	n/a
12	CUX1	chr1:46835380-46836461	K562	blood:	n/a	n/a
13	USF1	chr1:46835877-46836378	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAL1	chr1:46835852-46836217	K562	blood:	n/a	n/a
15	RUNX3	chr1:46835645-46836236	GM12878	blood:	n/a	n/a
16	ZMIZ1	chr1:46835710-46836146	K562	blood:	n/a	n/a
17	POLR2A	chr1:46835611-46836259	K562	blood:	n/a	n/a
18	POLR2A	chr1:46835920-46836106	HepG2	liver:	n/a	n/a
19	USF1	chr1:46835947-46836267	GM12878	blood:	n/a	n/a
20	RUNX3	chr1:46835795-46836264	GM12878	blood:	n/a	n/a
21	USF1	chr1:46835909-46836374	ECC-1	luminal epithelium:	n/a	n/a
22	EBF1	chr1:46835731-46836078	GM12878	blood:	n/a	chr1:46835924-46835935
23	EBF1	chr1:46835770-46836120	GM12878	blood:	n/a	chr1:46835924-46835935
24	MAZ	chr1:46835654-46836059	K562	blood:	n/a	n/a
25	BATF	chr1:46835879-46836383	GM12878	blood:	n/a	n/a
26	USF1	chr1:46835884-46836599	K562	blood:	n/a	n/a
27	POLR2A	chr1:46834969-46836255	K562	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46829128..46831471-chr1:46833892..46836194,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225779	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11211267	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11802856	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804220	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12086460	1.00[EUR][1000 genomes]
rs12096333	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35563048	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3931457	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6678791	0.99[AFR][1000 genomes]
rs6688130	0.83[AMR][1000 genomes]
rs6703596	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46807600-46844600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46809200-46848600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:46818200-46839400	Strong transcription	Dnd41	blood
4	chr1:46824600-46836200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:46826200-46836000	Strong transcription	Primary B cells from cord blood	blood
6	chr1:46827800-46837400	Weak transcription	Fetal Brain Male	brain
7	chr1:46828200-46836200	Weak transcription	Small Intestine	intestine
8	chr1:46828200-46836800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:46828200-46845400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:46828600-46843800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:46829000-46839800	Weak transcription	A549	lung
12	chr1:46829200-46836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:46829200-46840200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:46829200-46840400	Weak transcription	Gastric	stomach
15	chr1:46829200-46846400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:46829200-46847200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:46829200-46847600	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:46829200-46848000	Weak transcription	Ovary	ovary
19	chr1:46829400-46837800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:46829400-46839000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:46829400-46859400	Weak transcription	Brain Substantia Nigra	brain
22	chr1:46830000-46836800	Weak transcription	Colonic Mucosa	Colon
23	chr1:46830200-46842000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:46830600-46840600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:46830600-46848800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:46830800-46836000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:46830800-46841000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:46831000-46836000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:46831200-46837600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:46831400-46836600	Weak transcription	Fetal Lung	lung
31	chr1:46831400-46837600	Weak transcription	HSMM	muscle
32	chr1:46831400-46839400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:46831400-46840400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:46831600-46839200	Weak transcription	Brain Germinal Matrix	brain
35	chr1:46833400-46836200	Weak transcription	HUVEC	blood vessel
36	chr1:46833400-46845600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:46833600-46836600	Strong transcription	Primary T cells from cord blood	blood
38	chr1:46834400-46836000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:46834400-46840200	Weak transcription	Right Ventricle	heart
40	chr1:46834600-46836200	Enhancers	HepG2	liver
41	chr1:46834600-46837200	Weak transcription	Fetal Intestine Small	intestine
42	chr1:46834600-46837200	Weak transcription	Fetal Thymus	thymus
43	chr1:46834600-46838000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:46834600-46840400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:46834600-46840600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:46834600-46847800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:46834600-46859600	Weak transcription	Psoas Muscle	Psoas
48	chr1:46834800-46836000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:46834800-46836400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:46834800-46836400	Weak transcription	Esophagus	oesophagus

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