Variant report

Variant	rs6678831
Chromosome Location	chr1:45137703-45137704
allele	A/G
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	RUNX3	chr1:45137605-45138440	GM12878	blood:	n/a	n/a
2	SPI1	chr1:45137622-45138635	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:45137635-45138651	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:45137694-45138223	GM12891	blood:	n/a	n/a
5	MTA3	chr1:45137567-45138794	GM12878	blood:	n/a	n/a
6	YY1	chr1:45137627-45138237	GM12892	blood:	n/a	chr1:45138034-45138050 chr1:45137730-45137738
7	YY1	chr1:45137608-45138441	GM12878	blood:	n/a	chr1:45138034-45138050 chr1:45137730-45137738
8	PML	chr1:45137675-45138534	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:45137618-45138483	HL-60	blood:	n/a	n/a
10	SPI1	chr1:45137606-45138560	HL-60	blood:	n/a	n/a
11	NFIC	chr1:45137600-45138454	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:45137605-45138308	GM12892	blood:	n/a	n/a
13	CEBPB	chr1:45137586-45138479	GM12878	blood:	n/a	n/a
14	STAT5A	chr1:45137657-45138431	GM12878	blood:	n/a	chr1:45138067-45138079
15	POLR2A	chr1:45137667-45138759	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:45137632-45138382	HL-60	blood:	n/a	n/a
17	RUNX3	chr1:45137619-45138572	GM12878	blood:	n/a	n/a
18	MTA3	chr1:45137645-45138333	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	chr1:45102853..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: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1080838	1.00[ASN][1000 genomes]
rs11581074	0.90[EUR][1000 genomes]
rs11582807	0.90[EUR][1000 genomes]
rs12022097	0.83[EUR][1000 genomes]
rs2224403	1.00[ASN][1000 genomes]
rs3889696	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660818	0.90[EUR][1000 genomes]
rs4660821	0.90[EUR][1000 genomes]
rs4660822	0.90[EUR][1000 genomes]
rs61789885	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663584	0.83[EUR][1000 genomes]
rs6668870	0.90[EUR][1000 genomes]
rs72899527	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7512181	1.00[ASN][1000 genomes]
rs7512488	1.00[ASN][1000 genomes]
rs7539312	0.81[EUR][1000 genomes]
rs7549471	1.00[ASN][1000 genomes]
rs7549579	1.00[ASN][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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45104000-45138200	Weak transcription	Fetal Brain Male	brain
2	chr1:45115200-45137800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:45115800-45138000	Weak transcription	NHDF-Ad	bronchial
4	chr1:45117200-45137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:45117200-45138600	Weak transcription	Aorta	Aorta
6	chr1:45117400-45138000	Weak transcription	Left Ventricle	heart
7	chr1:45118600-45138600	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:45119200-45139200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:45119800-45138000	Weak transcription	Primary T cells from cord blood	blood
10	chr1:45121000-45138600	Weak transcription	Gastric	stomach
11	chr1:45125400-45137800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:45125400-45138000	Weak transcription	Fetal Brain Female	brain
13	chr1:45126200-45137800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:45126400-45137800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:45126400-45138200	Weak transcription	Fetal Lung	lung
16	chr1:45127800-45138400	Weak transcription	Small Intestine	intestine
17	chr1:45128400-45137800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:45128600-45137800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:45128600-45138000	Weak transcription	Ovary	ovary
20	chr1:45128800-45138000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:45129400-45138200	Weak transcription	Fetal Intestine Large	intestine
22	chr1:45129600-45138000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:45129600-45138000	Weak transcription	HepG2	liver
24	chr1:45130800-45138000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:45130800-45139000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:45130800-45139000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:45132600-45138000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:45132600-45138000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:45136000-45138600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:45136200-45138400	Weak transcription	Esophagus	oesophagus
31	chr1:45136200-45139000	Enhancers	Brain Cingulate Gyrus	brain
32	chr1:45136400-45137800	Weak transcription	Fetal Intestine Small	intestine
33	chr1:45136400-45138200	Enhancers	Brain Hippocampus Middle	brain
34	chr1:45136400-45138800	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:45136400-45139000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:45136400-45139200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr1:45136600-45139000	Enhancers	Brain Substantia Nigra	brain
38	chr1:45136800-45137800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:45136800-45137800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:45136800-45138600	Enhancers	Brain Anterior Caudate	brain
41	chr1:45136800-45139000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:45136800-45139200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:45136800-45139400	Enhancers	Primary B cells from peripheral blood	blood
44	chr1:45137000-45137800	Enhancers	Primary B cells from cord blood	blood
45	chr1:45137000-45137800	Enhancers	HSMMtube	muscle
46	chr1:45137000-45138000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:45137000-45138600	Weak transcription	Right Ventricle	heart
48	chr1:45137000-45138800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:45137000-45139400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:45137000-45139400	Enhancers	Spleen	Spleen

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