Variant report

Variant	rs56187338
Chromosome Location	chr1:160072697-160072698
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	NFIC	chr1:160072427-160072942	ECC-1	luminal epithelium:	n/a	n/a
2	EGR1	chr1:160072463-160072937	ECC-1	luminal epithelium:	n/a	chr1:160072710-160072732 chr1:160072716-160072726 chr1:160072714-160072728 chr1:160072716-160072725 chr1:160072716-160072727 chr1:160072716-160072726
3	EP300	chr1:160072341-160073511	ECC-1	luminal epithelium:	n/a	chr1:160072955-160072969
4	SPI1	chr1:160072681-160073097	HL-60	blood:	n/a	chr1:160073011-160073024
5	EGR1	chr1:160072399-160073019	ECC-1	luminal epithelium:	n/a	chr1:160072710-160072732 chr1:160072716-160072726 chr1:160072714-160072728 chr1:160072716-160072725 chr1:160072716-160072727 chr1:160072716-160072726
6	TCF12	chr1:160072480-160073400	ECC-1	luminal epithelium:	n/a	chr1:160073074-160073084 chr1:160072708-160072715

No.	Distal block	Cell Line	Cell type
1	chr1:160072053..160074281-chr1:160176013..160178605,2	K562	blood:
2	chr1:160072203..160074100-chr1:160344001..160347730,3	K562	blood:
3	chr1:160071459..160074798-chr1:160230293..160234240,4	K562	blood:
4	chr1:160071057..160072737-chr1:160310768..160312526,2	K562	blood:
5	chr1:160071153..160073617-chr1:160073631..160075783,2	MCF-7	breast:
6	chr1:160071920..160073465-chr1:160074068..160076478,2	K562	blood:
7	chr1:160068906..160070835-chr1:160071784..160074235,2	K562	blood:

Variant related genes	Relation type
IGSF8	TF binding region
ENSG00000228606	Chromatin interaction
ENSG00000132716	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11265317	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11265328	0.83[AFR][1000 genomes]
rs1131891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1186675	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12401984	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12402134	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12402888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12408584	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12727520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17846705	0.83[AFR][1000 genomes]
rs1884998	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747619	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41265757	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55753565	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211999	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61822013	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61822015	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs970365	0.81[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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160069200-160074800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:160069400-160073000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:160069400-160073600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:160069400-160075600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:160069400-160075600	Enhancers	Fetal Muscle Leg	muscle
6	chr1:160070400-160074600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:160070400-160074800	Enhancers	Fetal Muscle Trunk	muscle
8	chr1:160070400-160075000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:160070600-160074400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:160070600-160074400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:160070600-160074400	Enhancers	Fetal Brain Male	brain
12	chr1:160070600-160074800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:160070800-160072800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:160071000-160072800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr1:160071000-160072800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:160071000-160072800	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr1:160071000-160073000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:160071000-160073000	Enhancers	Psoas Muscle	Psoas
19	chr1:160071000-160073000	Enhancers	Osteobl	bone
20	chr1:160071000-160073200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:160071000-160073200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:160071000-160073200	Enhancers	A549	lung
23	chr1:160071000-160073400	Enhancers	Fetal Intestine Small	intestine
24	chr1:160071000-160074400	Enhancers	Ovary	ovary
25	chr1:160071000-160074600	Enhancers	Brain Germinal Matrix	brain
26	chr1:160071000-160074600	Enhancers	HSMM	muscle
27	chr1:160071000-160074800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:160071000-160074800	Enhancers	Fetal Lung	lung
29	chr1:160071000-160074800	Enhancers	Fetal Stomach	stomach
30	chr1:160071000-160074800	Enhancers	HSMMtube	muscle
31	chr1:160071200-160073000	Enhancers	Right Ventricle	heart
32	chr1:160071200-160074800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr1:160071200-160074800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:160071200-160077600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:160071400-160072800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:160071400-160072800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:160071400-160073000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:160071400-160073200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:160071400-160073200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr1:160071400-160073400	Enhancers	Brain Anterior Caudate	brain
41	chr1:160071400-160073800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:160071400-160074000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:160071400-160074000	Enhancers	Fetal Brain Female	brain
44	chr1:160071400-160074800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr1:160071400-160075400	Enhancers	Brain Substantia Nigra	brain
46	chr1:160071400-160075600	Enhancers	Brain Cingulate Gyrus	brain
47	chr1:160071400-160078400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:160071600-160072800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:160071600-160072800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:160071600-160073400	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links