Variant report

Variant	rs60766209
Chromosome Location	chr1:45229849-45229850
allele	A/C
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	POLR2A	chr1:45229385-45230447	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000225721	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12404244	0.89[ASN][1000 genomes]
rs12405110	0.80[ASN][1000 genomes]
rs12407627	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16832249	0.83[ASN][1000 genomes]
rs17391430	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3795712	0.91[EUR][1000 genomes]
rs3795715	0.93[EUR][1000 genomes]
rs3795718	0.85[ASN][1000 genomes]
rs3806398	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4073112	0.89[ASN][1000 genomes]
rs41269079	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55703843	0.93[EUR][1000 genomes]
rs58532407	0.85[EUR][1000 genomes]
rs58603818	0.85[EUR][1000 genomes]
rs59803789	0.87[ASN][1000 genomes]
rs59895800	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60452778	0.95[EUR][1000 genomes]
rs6657078	0.83[ASN][1000 genomes]
rs6678737	0.88[ASN][1000 genomes]
rs72674017	0.92[EUR][1000 genomes]
rs72674023	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72674049	0.83[ASN][1000 genomes]
rs72674051	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45205800-45240600	Weak transcription	Ovary	ovary
2	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
3	chr1:45206200-45230200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
6	chr1:45206400-45232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:45207000-45233800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:45207200-45234200	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr1:45207200-45234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:45207400-45233800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:45207600-45233800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:45207600-45234400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:45208600-45233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:45208600-45234000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:45208800-45234400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:45209400-45235200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:45211200-45233800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:45211400-45233600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr1:45211400-45234800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:45211400-45235000	Strong transcription	Fetal Stomach	stomach
24	chr1:45211600-45231200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:45211600-45234600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:45211600-45235200	Strong transcription	Thymus	Thymus
27	chr1:45212000-45235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:45212000-45235200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:45212400-45234800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:45212400-45235000	Strong transcription	Fetal Thymus	thymus
31	chr1:45214400-45240400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:45215200-45231000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:45215600-45233600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:45217800-45233400	Strong transcription	Fetal Intestine Small	intestine
35	chr1:45218000-45240600	Weak transcription	Small Intestine	intestine
36	chr1:45218200-45230000	Strong transcription	Osteobl	bone
37	chr1:45218200-45230200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:45218200-45230200	Strong transcription	HepG2	liver
39	chr1:45218200-45232600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:45218200-45233600	Strong transcription	Dnd41	blood
41	chr1:45218200-45233800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:45218400-45230000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:45218600-45230000	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr1:45219000-45233800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:45219200-45235200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:45219200-45240600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:45219200-45240800	Weak transcription	Gastric	stomach
48	chr1:45219600-45234600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:45223600-45234400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:45223600-45234800	Weak transcription	Fetal Kidney	kidney

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