Variant report

Variant	rs3889696
Chromosome Location	chr1:45138199-45138200
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	IKZF1	chr1:45137760-45138663	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:45137818-45138228	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:45137605-45138440	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:45137833-45138353	GM12891	blood:	n/a	n/a
5	MYC	chr1:45138004-45138268	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:45137827-45138404	PFSK-1	brain:	n/a	n/a
7	FOSL1	chr1:45137906-45138312	K562	blood:	n/a	chr1:45138098-45138109 chr1:45138101-45138111 chr1:45138101-45138111
8	FOS	chr1:45137929-45138280	MCF10A-Er-Src	breast:	n/a	chr1:45138098-45138109 chr1:45138101-45138111 chr1:45138100-45138111 chr1:45138101-45138111
9	TBP	chr1:45137869-45138266	GM12878	blood:	n/a	n/a
10	PML	chr1:45137922-45138267	GM12878	blood:	n/a	n/a
11	SPI1	chr1:45137622-45138635	GM12878	blood:	n/a	n/a
12	NFATC1	chr1:45137775-45138367	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:45137791-45138262	GM12892	blood:	n/a	n/a
14	SPI1	chr1:45137819-45138357	GM12878	blood:	n/a	n/a
15	YY1	chr1:45137763-45138213	GM12878	blood:	n/a	chr1:45138034-45138050
16	TEAD4	chr1:45137873-45138342	K562	blood:	n/a	n/a
17	RCOR1	chr1:45138028-45138220	K562	blood:	n/a	n/a
18	MAX	chr1:45138136-45138221	K562	blood:	n/a	n/a
19	STAT3	chr1:45137973-45138293	MCF10A-Er-Src	breast:	n/a	chr1:45138067-45138079
20	ELF1	chr1:45137878-45138420	K562	blood:	n/a	n/a
21	ELK1	chr1:45138102-45138301	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:45137635-45138651	GM12892	blood:	n/a	n/a
23	FOXM1	chr1:45137765-45138330	GM12878	blood:	n/a	n/a
24	TBL1XR1	chr1:45137774-45138292	GM12878	blood:	n/a	n/a
25	CHD1	chr1:45137772-45138291	GM12878	blood:	n/a	n/a
26	REST	chr1:45138091-45138291	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:45137694-45138223	GM12891	blood:	n/a	n/a
28	RCOR1	chr1:45138011-45138332	GM12878	blood:	n/a	n/a
29	FOXM1	chr1:45137777-45138350	GM12878	blood:	n/a	n/a
30	JUN	chr1:45137752-45138383	K562	blood:	n/a	chr1:45138098-45138109 chr1:45138101-45138111 chr1:45138101-45138111
31	MTA3	chr1:45137567-45138794	GM12878	blood:	n/a	n/a
32	ELF1	chr1:45137760-45138407	GM12878	blood:	n/a	n/a
33	FOS	chr1:45137962-45138269	MCF10A-Er-Src	breast:	n/a	chr1:45138098-45138109 chr1:45138101-45138111 chr1:45138100-45138111 chr1:45138101-45138111
34	BCL11A	chr1:45137952-45138265	GM12878	blood:	n/a	n/a
35	YY1	chr1:45137627-45138237	GM12892	blood:	n/a	chr1:45138034-45138050 chr1:45137730-45137738
36	STAT3	chr1:45138131-45138354	MCF10A-Er-Src	breast:	n/a	n/a
37	ATF2	chr1:45137931-45138310	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:45137898-45138531	HUVEC	blood vessel:	n/a	n/a
39	YY1	chr1:45137608-45138441	GM12878	blood:	n/a	chr1:45138034-45138050 chr1:45137730-45137738
40	BCL11A	chr1:45137878-45138299	GM12878	blood:	n/a	n/a
41	CTCF	chr1:45138120-45138270	HAc	cerebellar:	n/a	n/a
42	PML	chr1:45137675-45138534	GM12878	blood:	n/a	n/a
43	FOS	chr1:45137951-45138294	MCF10A-Er-Src	breast:	n/a	chr1:45138098-45138109 chr1:45138101-45138111 chr1:45138100-45138111 chr1:45138101-45138111
44	MYC	chr1:45137793-45138400	NB4	blood:	n/a	n/a
45	BCLAF1	chr1:45137809-45138395	GM12878	blood:	n/a	n/a
46	EBF1	chr1:45137940-45138357	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:45137618-45138483	HL-60	blood:	n/a	n/a
48	MAX	chr1:45137796-45138236	GM12878	blood:	n/a	n/a
49	IRF4	chr1:45137784-45138276	GM12878	blood:	n/a	n/a
50	FAM48A	chr1:45137843-45138238	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45095169..45100377-chr1:45133934..45142864,15	K562	blood:
2	chr1:45136867..45139801-chr1:45184892..45187716,2	MCF-7	breast:
3	chr1:45100701..45102574-chr1:45138081..45139709,2	K562	blood:
4	chr1:45102853..45104841-chr1:45137673..45140474,2	K562	blood:

Variant related genes	Relation type
C1orf228	TF binding region
ENSG00000199377	Chromatin interaction
ENSG00000187147	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11581074	0.93[EUR][1000 genomes]
rs11582807	0.93[EUR][1000 genomes]
rs12022097	0.85[EUR][1000 genomes]
rs4660818	0.93[EUR][1000 genomes]
rs4660821	0.93[EUR][1000 genomes]
rs4660822	0.92[EUR][1000 genomes]
rs61789885	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6663584	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6668870	0.93[EUR][1000 genomes]
rs6678831	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72899527	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7539312	0.84[EUR][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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45104000-45138200	Weak transcription	Fetal Brain Male	brain
2	chr1:45117200-45138600	Weak transcription	Aorta	Aorta
3	chr1:45118600-45138600	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:45119200-45139200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:45121000-45138600	Weak transcription	Gastric	stomach
6	chr1:45126400-45138200	Weak transcription	Fetal Lung	lung
7	chr1:45127800-45138400	Weak transcription	Small Intestine	intestine
8	chr1:45129400-45138200	Weak transcription	Fetal Intestine Large	intestine
9	chr1:45130800-45139000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:45130800-45139000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:45136000-45138600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:45136200-45138400	Weak transcription	Esophagus	oesophagus
13	chr1:45136200-45139000	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:45136400-45138200	Enhancers	Brain Hippocampus Middle	brain
15	chr1:45136400-45138800	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:45136400-45139000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:45136400-45139200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:45136600-45139000	Enhancers	Brain Substantia Nigra	brain
19	chr1:45136800-45138600	Enhancers	Brain Anterior Caudate	brain
20	chr1:45136800-45139000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:45136800-45139200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:45136800-45139400	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:45137000-45138600	Weak transcription	Right Ventricle	heart
24	chr1:45137000-45138800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:45137000-45139400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:45137000-45139400	Enhancers	Spleen	Spleen
27	chr1:45137200-45138600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:45137200-45139000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:45137400-45139200	Enhancers	Placenta	Placenta
30	chr1:45137400-45139200	Enhancers	Fetal Thymus	thymus
31	chr1:45137400-45139400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:45137400-45139800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr1:45137600-45138200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr1:45137600-45138600	Enhancers	Liver	Liver
35	chr1:45137600-45138600	Enhancers	Duodenum Mucosa	Duodenum
36	chr1:45137600-45138600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:45137600-45138600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:45137600-45138800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:45137600-45138800	Enhancers	Brain Angular Gyrus	brain
40	chr1:45137600-45138800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:45137600-45139000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:45137600-45139000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:45137600-45139000	Enhancers	HMEC	breast
44	chr1:45137600-45139000	Enhancers	Osteobl	bone
45	chr1:45137600-45139200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:45137600-45139200	Enhancers	Fetal Muscle Trunk	muscle
47	chr1:45137600-45139200	Enhancers	Fetal Muscle Leg	muscle
48	chr1:45137600-45139200	Enhancers	Fetal Stomach	stomach
49	chr1:45137600-45139200	Enhancers	Right Atrium	heart
50	chr1:45137600-45139200	Enhancers	Stomach Mucosa	stomach

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