Variant report

Variant	rs55780668
Chromosome Location	chr1:160040074-160040075
allele	G/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	ZBTB7A	chr1:160039916-160040230	K562	blood:	n/a	n/a
2	TCF12	chr1:160040058-160040673	ECC-1	luminal epithelium:	n/a	n/a
3	SP2	chr1:160040043-160040228	H1-hESC	embryonic stem cell:	n/a	chr1:160040110-160040120
4	CEBPD	chr1:160039739-160040314	HepG2	liver:	n/a	n/a
5	ELF1	chr1:160040068-160040291	HepG2	liver:	n/a	n/a
6	SP1	chr1:160039929-160040469	H1-hESC	embryonic stem cell:	n/a	chr1:160040382-160040396 chr1:160040169-160040178 chr1:160040169-160040178 chr1:160040168-160040177 chr1:160040167-160040178 chr1:160040167-160040179 chr1:160040168-160040178 chr1:160040164-160040178 chr1:160040387-160040396 chr1:160040168-160040178 chr1:160040108-160040129 chr1:160040385-160040397 chr1:160040167-160040179 chr1:160040386-160040395 chr1:160040385-160040397 chr1:160040381-160040394
7	EGR1	chr1:160039932-160040202	K562	blood:	n/a	chr1:160040168-160040178 chr1:160040012-160040026 chr1:160040163-160040176 chr1:160040085-160040099
8	ZBTB7A	chr1:160039696-160040461	ECC-1	luminal epithelium:	n/a	n/a
9	EGR1	chr1:160039937-160040171	GM12878	blood:	n/a	chr1:160040012-160040026 chr1:160040085-160040099
10	ZBTB7A	chr1:160039866-160040082	HepG2	liver:	n/a	n/a
11	ZBTB7A	chr1:160039748-160040595	ECC-1	luminal epithelium:	n/a	n/a
12	GATA2	chr1:160039730-160040821	SH-SY5Y	brain:	n/a	chr1:160039945-160039954 chr1:160040637-160040646 chr1:160039945-160039955 chr1:160040639-160040646 chr1:160039936-160039953 chr1:160039947-160039954 chr1:160039944-160039956
13	NFYB	chr1:160039960-160040319	GM12878	blood:	n/a	chr1:160040107-160040121 chr1:160040107-160040122

Variant related genes	Relation type
KCNJ10	TF binding region

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11265317	0.83[AMR][1000 genomes]
rs1186675	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12408584	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56211999	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821993	0.80[EUR][1000 genomes]
rs61822013	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61822015	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs970365	0.86[AMR][1000 genomes];0.81[EUR][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	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 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	chr1:160037400-160040200	Weak transcription	Fetal Kidney	kidney
2	chr1:160037600-160040800	Active TSS	Brain Angular Gyrus	brain
3	chr1:160037800-160040600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:160038000-160040200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:160038000-160040600	Active TSS	Brain Cingulate Gyrus	brain
6	chr1:160038000-160041000	Active TSS	Brain Hippocampus Middle	brain
7	chr1:160038200-160040600	Active TSS	Brain Anterior Caudate	brain
8	chr1:160038200-160040800	Active TSS	Brain Substantia Nigra	brain
9	chr1:160039200-160040600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:160039400-160040200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr1:160039400-160040200	Enhancers	Fetal Brain Male	brain
12	chr1:160039400-160040400	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr1:160039400-160040400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:160039400-160040600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:160039400-160040800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:160039400-160041000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:160039600-160040200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:160039600-160040200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr1:160039600-160040200	Bivalent Enhancer	Primary B cells from cord blood	blood
20	chr1:160039600-160040200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:160039600-160040200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:160039600-160040200	Bivalent Enhancer	Adipose Nuclei	Adipose
23	chr1:160039600-160040200	Bivalent Enhancer	Placenta	Placenta
24	chr1:160039600-160040200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:160039600-160040200	Active TSS	HepG2	liver
26	chr1:160039600-160040200	Bivalent Enhancer	HUVEC	blood vessel
27	chr1:160039600-160040400	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
28	chr1:160039600-160040400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:160039600-160040600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr1:160039600-160040600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:160039600-160040800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:160039600-160040800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
33	chr1:160039600-160041000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:160039600-160041200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:160039800-160040200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:160039800-160040200	Enhancers	Primary hematopoietic stem cells	blood
37	chr1:160039800-160040200	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:160039800-160040200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:160039800-160040200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:160039800-160040200	Bivalent Enhancer	Fetal Intestine Large	intestine
41	chr1:160039800-160040200	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:160039800-160040200	Weak transcription	Spleen	Spleen
43	chr1:160039800-160040400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:160039800-160040400	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:160039800-160040400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:160039800-160040400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:160039800-160040400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
48	chr1:160039800-160040400	Active TSS	Brain Germinal Matrix	brain
49	chr1:160039800-160040400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
50	chr1:160039800-160040600	Active TSS	H1 Cell Line	embryonic stem cell

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