Variant report

Variant	rs3765879
Chromosome Location	chr1:210532035-210532036
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	FOS	chr1:210532018-210532127	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr1:210531932-210532341	H1-hESC	embryonic stem cell:	n/a	chr1:210532051-210532062 chr1:210532051-210532062
3	MYC	chr1:210531979-210532135	MCF10A-Er-Src	breast:	n/a	chr1:210532051-210532062 chr1:210532051-210532062
4	POLR2A	chr1:210531656-210532086	K562	blood:	n/a	n/a
5	USF1	chr1:210531817-210532177	H1-hESC	embryonic stem cell:	n/a	chr1:210532052-210532061 chr1:210532053-210532062 chr1:210532052-210532061 chr1:210532051-210532060 chr1:210532046-210532067
6	USF1	chr1:210531926-210532202	H1-hESC	embryonic stem cell:	n/a	chr1:210532052-210532061 chr1:210532053-210532062 chr1:210532052-210532061 chr1:210532051-210532060 chr1:210532046-210532067
7	FOS	chr1:210531991-210532121	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr1:210531962-210532250	MCF10A-Er-Src	breast:	n/a	chr1:210532051-210532062 chr1:210532051-210532062

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210502542..210504337-chr1:210530347..210534050,4	MCF-7	breast:
2	chr1:210531383..210533438-chr1:210535536..210538131,3	K562	blood:

Variant related genes	Relation type
HHAT	TF binding region
ENSG00000054392	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10489388	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12729428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17016026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17759021	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890303	0.83[JPT][hapmap]
rs2357583	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3765872	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3765884	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs60935759	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61828656	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540589	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6656628	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6656669	0.84[CEU][hapmap]
rs6669428	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6677509	0.89[CEU][hapmap]
rs6690120	0.89[CEU][hapmap]
rs6697682	0.83[JPT][hapmap]
rs7354957	0.84[EUR][1000 genomes]
rs7355019	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs742560	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7527939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7530104	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7550408	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550554	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs761171	0.89[CEU][hapmap];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:210513000-210540400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:210516800-210534400	Weak transcription	Fetal Lung	lung
4	chr1:210517000-210534400	Weak transcription	HSMM	muscle
5	chr1:210517200-210534400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:210517200-210534400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:210517200-210534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:210517200-210535800	Weak transcription	Right Ventricle	heart
9	chr1:210517200-210536000	Weak transcription	Fetal Stomach	stomach
10	chr1:210517200-210536000	Weak transcription	Left Ventricle	heart
11	chr1:210517400-210533200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:210517400-210534400	Weak transcription	Adipose Nuclei	Adipose
13	chr1:210517600-210536000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:210518600-210534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:210521000-210534400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:210521200-210534400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:210521400-210534400	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:210522600-210537600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:210523000-210534400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:210525200-210538000	Weak transcription	Ovary	ovary
21	chr1:210526000-210534400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:210526200-210534600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:210527800-210534600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:210528400-210536600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:210529400-210534400	Weak transcription	Brain Substantia Nigra	brain
26	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
27	chr1:210531200-210533400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:210531400-210532400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:210531400-210532400	Enhancers	Fetal Heart	heart
30	chr1:210531400-210532600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:210531400-210532600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:210531400-210532800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:210531400-210532800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:210531400-210532800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr1:210531400-210532800	Enhancers	Brain Germinal Matrix	brain
36	chr1:210531400-210533000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr1:210531400-210533200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:210531600-210532400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:210531600-210532400	Enhancers	HUVEC	blood vessel
40	chr1:210531600-210532600	Enhancers	Stomach Mucosa	stomach
41	chr1:210531800-210532200	Enhancers	H9 Cell Line	embryonic stem cell
42	chr1:210531800-210532600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:210531800-210532600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr1:210531800-210533000	Enhancers	HSMMtube	muscle
45	chr1:210532000-210532400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr1:210532000-210532600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr1:210532000-210533200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:210532000-210533200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:210532000-210533200	Enhancers	Liver	Liver
50	chr1:210532000-210534400	Weak transcription	Brain Hippocampus Middle	brain

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