Variant report

Variant	rs3889695
Chromosome Location	chr1:45137893-45137894
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	POLR2A	chr1:45137827-45138404	PFSK-1	brain:	n/a	n/a
6	TBP	chr1:45137869-45138266	GM12878	blood:	n/a	n/a
7	SPI1	chr1:45137622-45138635	GM12878	blood:	n/a	n/a
8	NFATC1	chr1:45137775-45138367	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:45137791-45138262	GM12892	blood:	n/a	n/a
10	SPI1	chr1:45137819-45138357	GM12878	blood:	n/a	n/a
11	YY1	chr1:45137763-45138213	GM12878	blood:	n/a	chr1:45138034-45138050
12	TEAD4	chr1:45137873-45138342	K562	blood:	n/a	n/a
13	PAX5	chr1:45137837-45138155	GM12878	blood:	n/a	n/a
14	ELF1	chr1:45137878-45138420	K562	blood:	n/a	n/a
15	POLR2A	chr1:45137635-45138651	GM12892	blood:	n/a	n/a
16	FOXM1	chr1:45137765-45138330	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr1:45137774-45138292	GM12878	blood:	n/a	n/a
18	CHD1	chr1:45137772-45138291	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:45137694-45138223	GM12891	blood:	n/a	n/a
20	FOXM1	chr1:45137777-45138350	GM12878	blood:	n/a	n/a
21	JUN	chr1:45137752-45138383	K562	blood:	n/a	chr1:45138098-45138109 chr1:45138101-45138111 chr1:45138101-45138111
22	MTA3	chr1:45137567-45138794	GM12878	blood:	n/a	n/a
23	ELF1	chr1:45137760-45138407	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:45137839-45138102	GM12891	blood:	n/a	n/a
25	YY1	chr1:45137627-45138237	GM12892	blood:	n/a	chr1:45138034-45138050 chr1:45137730-45137738
26	WRNIP1	chr1:45137772-45138161	GM12878	blood:	n/a	n/a
27	YY1	chr1:45137608-45138441	GM12878	blood:	n/a	chr1:45138034-45138050 chr1:45137730-45137738
28	BCL11A	chr1:45137878-45138299	GM12878	blood:	n/a	n/a
29	PML	chr1:45137675-45138534	GM12878	blood:	n/a	n/a
30	MYC	chr1:45137793-45138400	NB4	blood:	n/a	n/a
31	BCLAF1	chr1:45137809-45138395	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:45137618-45138483	HL-60	blood:	n/a	n/a
33	MAX	chr1:45137796-45138236	GM12878	blood:	n/a	n/a
34	IRF4	chr1:45137784-45138276	GM12878	blood:	n/a	n/a
35	FAM48A	chr1:45137843-45138238	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:45137893-45138153	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:45137727-45138399	GM12878	blood:	n/a	n/a
38	POU2F2	chr1:45137780-45138310	GM12878	blood:	n/a	n/a
39	MAX	chr1:45137705-45138353	NB4	blood:	n/a	n/a
40	NFYB	chr1:45137845-45138284	GM12878	blood:	n/a	n/a
41	BATF	chr1:45137828-45138292	GM12878	blood:	n/a	chr1:45138103-45138113
42	SP1	chr1:45137838-45138272	GM12878	blood:	n/a	chr1:45137850-45137864
43	SPI1	chr1:45137606-45138560	HL-60	blood:	n/a	n/a
44	YY1	chr1:45137831-45138370	GM12891	blood:	n/a	chr1:45138034-45138050
45	NFIC	chr1:45137600-45138454	GM12878	blood:	n/a	n/a
46	EP300	chr1:45137872-45138317	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:45137605-45138308	GM12892	blood:	n/a	n/a
48	NFIC	chr1:45137770-45138409	GM12878	blood:	n/a	n/a
49	CEBPB	chr1:45137586-45138479	GM12878	blood:	n/a	n/a
50	STAT5A	chr1:45137657-45138431	GM12878	blood:	n/a	chr1:45138067-45138079

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	chr1:45102853..45104841-chr1:45137673..45140474,2	K562	blood:

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

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12036630	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16832186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16832188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3444	0.89[CHD][hapmap]
rs3738733	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754421	0.90[EUR][1000 genomes]
rs3768438	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3768439	0.89[CHD][hapmap]
rs3768441	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3850854	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41468751	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs41524944	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4660284	0.89[CHD][hapmap]
rs4660286	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4660814	0.90[EUR][1000 genomes]
rs4660819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660820	0.90[AMR][1000 genomes]
rs56756630	0.90[EUR][1000 genomes]
rs59834392	0.90[EUR][1000 genomes]
rs66509359	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671943	0.90[EUR][1000 genomes]
rs72671944	0.90[EUR][1000 genomes]
rs72671945	0.90[EUR][1000 genomes]
rs72671948	0.90[EUR][1000 genomes]
rs72671950	0.90[EUR][1000 genomes]
rs72671962	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671966	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671967	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671971	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72671982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72671984	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72671988	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539607	1.00[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:102 , 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	chr1:45115800-45138000	Weak transcription	NHDF-Ad	bronchial
3	chr1:45117200-45138600	Weak transcription	Aorta	Aorta
4	chr1:45117400-45138000	Weak transcription	Left Ventricle	heart
5	chr1:45118600-45138600	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:45119200-45139200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:45119800-45138000	Weak transcription	Primary T cells from cord blood	blood
8	chr1:45121000-45138600	Weak transcription	Gastric	stomach
9	chr1:45125400-45138000	Weak transcription	Fetal Brain Female	brain
10	chr1:45126400-45138200	Weak transcription	Fetal Lung	lung
11	chr1:45127800-45138400	Weak transcription	Small Intestine	intestine
12	chr1:45128600-45138000	Weak transcription	Ovary	ovary
13	chr1:45128800-45138000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:45129400-45138200	Weak transcription	Fetal Intestine Large	intestine
15	chr1:45129600-45138000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:45129600-45138000	Weak transcription	HepG2	liver
17	chr1:45130800-45138000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:45130800-45139000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:45130800-45139000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:45132600-45138000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:45132600-45138000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:45136000-45138600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:45136200-45138400	Weak transcription	Esophagus	oesophagus
24	chr1:45136200-45139000	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:45136400-45138200	Enhancers	Brain Hippocampus Middle	brain
26	chr1:45136400-45138800	Enhancers	Primary hematopoietic stem cells	blood
27	chr1:45136400-45139000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:45136400-45139200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:45136600-45139000	Enhancers	Brain Substantia Nigra	brain
30	chr1:45136800-45138600	Enhancers	Brain Anterior Caudate	brain
31	chr1:45136800-45139000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:45136800-45139200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:45136800-45139400	Enhancers	Primary B cells from peripheral blood	blood
34	chr1:45137000-45138000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr1:45137000-45138600	Weak transcription	Right Ventricle	heart
36	chr1:45137000-45138800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:45137000-45139400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:45137000-45139400	Enhancers	Spleen	Spleen
39	chr1:45137200-45138600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:45137200-45139000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:45137400-45139200	Enhancers	Placenta	Placenta
42	chr1:45137400-45139200	Enhancers	Fetal Thymus	thymus
43	chr1:45137400-45139400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:45137400-45139800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr1:45137600-45138200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr1:45137600-45138600	Enhancers	Liver	Liver
47	chr1:45137600-45138600	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:45137600-45138600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:45137600-45138600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr1:45137600-45138800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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