Variant report

Variant	rs13012704
Chromosome Location	chr2:38918793-38918794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38828223..38831586-chr2:38916427..38918985,3	MCF-7	breast:
2	chr2:38915899..38920812-chr2:38977039..38979793,4	K562	blood:
3	chr2:38918111..38919788-chr2:38928353..38930489,2	K562	blood:
4	chr2:38909532..38914838-chr2:38917160..38922190,4	K562	blood:
5	chr17:62340495..62341314-chr2:38918193..38919071,2	MCF-7	breast:
6	chr2:38917783..38919456-chr2:38977277..38979712,2	MCF-7	breast:
7	chr2:38872329..38875260-chr2:38918256..38921155,2	K562	blood:
8	chr2:38828129..38829795-chr2:38916759..38919645,2	K562	blood:
9	chr2:38917976..38920812-chr2:38977039..38979793,2	K562	blood:
10	chr2:38816136..38818407-chr2:38916717..38919701,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000136478	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10203706	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12469458	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12469534	0.93[EUR][1000 genomes]
rs12712612	0.93[EUR][1000 genomes]
rs13004674	0.90[EUR][1000 genomes]
rs13004806	0.93[EUR][1000 genomes]
rs13004842	0.93[EUR][1000 genomes]
rs13005073	0.93[EUR][1000 genomes]
rs13006376	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13010022	0.95[EUR][1000 genomes]
rs13016907	0.95[EUR][1000 genomes]
rs13383762	0.95[EUR][1000 genomes]
rs17576472	0.93[EUR][1000 genomes]
rs17576507	0.95[EUR][1000 genomes]
rs28716236	0.95[EUR][1000 genomes]
rs34391548	0.93[EUR][1000 genomes]
rs34558770	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34756536	0.95[EUR][1000 genomes]
rs34875979	0.98[EUR][1000 genomes]
rs34909144	0.98[EUR][1000 genomes]
rs35448554	0.95[EUR][1000 genomes]
rs35585199	0.93[EUR][1000 genomes]
rs4670885	0.95[EUR][1000 genomes]
rs58757994	0.93[EUR][1000 genomes]
rs6707421	0.83[ASN][1000 genomes]
rs6741892	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74177081	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894200-38919000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
3	chr2:38894600-38919600	Weak transcription	Fetal Heart	heart
4	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:38898600-38921200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:38905200-38920400	Strong transcription	Fetal Intestine Large	intestine
11	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
12	chr2:38906400-38918800	Strong transcription	Duodenum Mucosa	Duodenum
13	chr2:38909200-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
15	chr2:38909400-38921200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:38909400-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
19	chr2:38909800-38938600	Weak transcription	Fetal Kidney	kidney
20	chr2:38910000-38948000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:38911000-38919000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:38911600-38920600	Strong transcription	Thymus	Thymus
23	chr2:38912600-38920800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:38912600-38921000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:38912600-38932000	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:38912800-38924200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:38913200-38919200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:38913200-38919800	Weak transcription	Gastric	stomach
29	chr2:38913800-38938800	Weak transcription	Fetal Brain Male	brain
30	chr2:38914200-38919800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:38914400-38930000	Weak transcription	Left Ventricle	heart
32	chr2:38914600-38921200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:38914600-38922800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:38914600-38935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:38914600-38938600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:38914600-38948000	Weak transcription	Spleen	Spleen
37	chr2:38915800-38947200	Weak transcription	Ovary	ovary
38	chr2:38916200-38918800	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:38916200-38921200	Genic enhancers	HepG2	liver
40	chr2:38916400-38918800	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr2:38916400-38918800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr2:38916400-38918800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:38916400-38919000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:38916400-38919400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:38916400-38920400	Enhancers	K562	blood
46	chr2:38916600-38918800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:38916600-38919600	Weak transcription	Fetal Stomach	stomach
48	chr2:38916600-38919800	Enhancers	NHLF	lung
49	chr2:38916600-38932600	Weak transcription	Lung	lung
50	chr2:38916800-38920000	Strong transcription	Primary B cells from peripheral blood	blood

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