Variant report

Variant	rs56229381
Chromosome Location	chr18:45453855-45453856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:45453701-45453915	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr18:45453779-45453919	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr18:45453154-45453962	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr18:45453762-45453930	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr18:45453448-45453910	GM12892	blood:	n/a	n/a
6	EGR1	chr18:45453844-45454050	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:45370062..45371817-chr18:45453252..45455227,2	MCF-7	breast:
2	chr18:45445551..45451271-chr18:45453158..45456977,7	K562	blood:
3	chr18:45425101..45428042-chr18:45452196..45454277,2	MCF-7	breast:
4	chr18:45451758..45454511-chr18:45455218..45457678,2	MCF-7	breast:
5	chr18:45412744..45415150-chr18:45452720..45455335,2	MCF-7	breast:
6	chr18:45450692..45455196-chr18:45455930..45459309,6	MCF-7	breast:
7	chr18:45439039..45441634-chr18:45452955..45455422,2	MCF-7	breast:
8	chr18:45452201..45455106-chr18:45476820..45479374,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMAD2	TF binding region
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs55709523	1.00[AMR][1000 genomes]
rs57068919	1.00[AMR][1000 genomes]
rs58270038	1.00[AMR][1000 genomes]
rs58295111	1.00[AMR][1000 genomes]
rs60628515	1.00[AMR][1000 genomes]
rs73439737	1.00[AMR][1000 genomes]
rs73439740	1.00[AMR][1000 genomes]
rs73439744	1.00[AMR][1000 genomes]
rs73439749	1.00[AMR][1000 genomes]
rs73439750	1.00[AMR][1000 genomes]
rs73439768	1.00[AMR][1000 genomes]
rs73439776	1.00[AMR][1000 genomes]
rs73439785	1.00[AMR][1000 genomes]
rs73439787	1.00[AMR][1000 genomes]
rs73439800	1.00[AMR][1000 genomes]
rs73441731	1.00[AMR][1000 genomes]
rs73441746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73441792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73441797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73443904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73443909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73443953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953296	1.00[AMR][1000 genomes]
rs73953298	1.00[AMR][1000 genomes]
rs73953299	1.00[AMR][1000 genomes]
rs8083595	1.00[AMR][1000 genomes]
rs8098327	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv909615	chr18:45452321-45493026	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45433200-45455000	Weak transcription	Fetal Stomach	stomach
2	chr18:45433200-45455400	Weak transcription	Fetal Brain Male	brain
3	chr18:45434000-45454600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr18:45435600-45455800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:45438600-45454600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr18:45439000-45456200	Weak transcription	Esophagus	oesophagus
7	chr18:45439000-45456200	Weak transcription	Spleen	Spleen
8	chr18:45439600-45455400	Weak transcription	Fetal Muscle Leg	muscle
9	chr18:45439800-45454600	Weak transcription	Fetal Intestine Large	intestine
10	chr18:45439800-45456200	Weak transcription	Pancreas	Pancrea
11	chr18:45442000-45454800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr18:45442400-45455000	Weak transcription	HSMM	muscle
13	chr18:45442600-45454600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr18:45442800-45454400	Weak transcription	NHDF-Ad	bronchial
15	chr18:45443000-45456000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr18:45443600-45455000	Weak transcription	Osteobl	bone
17	chr18:45444400-45454400	Enhancers	Primary T cells from cord blood	blood
18	chr18:45444800-45456000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr18:45444800-45456000	Weak transcription	Lung	lung
20	chr18:45446000-45455400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr18:45446200-45454400	Weak transcription	Fetal Kidney	kidney
22	chr18:45446200-45455800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr18:45447600-45456000	Weak transcription	Left Ventricle	heart
24	chr18:45448400-45454400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr18:45449400-45454800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr18:45450000-45454400	Weak transcription	Primary B cells from cord blood	blood
27	chr18:45450000-45456200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr18:45450200-45454600	Weak transcription	Ovary	ovary
29	chr18:45450200-45454800	Weak transcription	Right Atrium	heart
30	chr18:45450200-45455200	Weak transcription	Right Ventricle	heart
31	chr18:45450800-45455000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr18:45451000-45455600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr18:45451000-45455600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr18:45451200-45454600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr18:45451200-45454600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr18:45451200-45454800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr18:45451200-45454800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr18:45451200-45454800	Enhancers	HepG2	liver
39	chr18:45451400-45454400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr18:45451400-45454600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr18:45451600-45455000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr18:45451600-45455200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr18:45451600-45456000	Enhancers	Fetal Heart	heart
44	chr18:45451800-45454600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr18:45451800-45454800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr18:45452000-45454200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr18:45452000-45454600	Enhancers	Colon Smooth Muscle	Colon
48	chr18:45452000-45456000	Enhancers	Brain Hippocampus Middle	brain
49	chr18:45452200-45454000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr18:45452200-45454000	Enhancers	Sigmoid Colon	Sigmoid Colon

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