Variant report

Variant	rs34909144
Chromosome Location	chr2:38917590-38917591
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 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	chr2:38914950..38917916-chr2:38919871..38923223,3	K562	blood:
4	chr2:38909532..38914838-chr2:38917160..38922190,4	K562	blood:
5	chr2:38912803..38914727-chr2:38916699..38918326,2	MCF-7	breast:
6	chr2:38828129..38829795-chr2:38916759..38919645,2	K562	blood:
7	chr2:38816136..38818407-chr2:38916717..38919701,2	K562	blood:
8	chr2:38868989..38871119-chr2:38916647..38918525,3	K562	blood:

No data

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

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12469458	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12469534	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712612	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13004674	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13004806	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13004842	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13005073	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13006376	0.97[EUR][1000 genomes]
rs13010022	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13012704	0.98[EUR][1000 genomes]
rs13016907	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13032255	0.81[ASN][1000 genomes]
rs13383762	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17576472	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17576507	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28716236	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34391548	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34533539	0.90[ASN][1000 genomes]
rs34558770	0.95[EUR][1000 genomes]
rs34756536	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34875979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35448554	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35585199	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670885	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58757994	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707543	0.81[ASN][1000 genomes]
rs6736380	0.81[ASN][1000 genomes]
rs6741892	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894000-38917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:38894200-38919000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:38894400-38917600	Weak transcription	NHDF-Ad	bronchial
4	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:38894600-38919600	Weak transcription	Fetal Heart	heart
6	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:38895000-38917600	Weak transcription	HSMM	muscle
8	chr2:38898600-38921200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:38903800-38918600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:38904400-38918400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:38905000-38917800	Weak transcription	Esophagus	oesophagus
14	chr2:38905000-38918400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:38905200-38920400	Strong transcription	Fetal Intestine Large	intestine
18	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
19	chr2:38905600-38917600	Strong transcription	Fetal Intestine Small	intestine
20	chr2:38906400-38918800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr2:38908800-38917600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:38909000-38918000	Weak transcription	Colonic Mucosa	Colon
23	chr2:38909200-38917600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:38909200-38917600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:38909200-38917800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:38909200-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
28	chr2:38909400-38921200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:38909400-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
32	chr2:38909800-38938600	Weak transcription	Fetal Kidney	kidney
33	chr2:38910000-38948000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:38910400-38917600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:38911000-38919000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:38911600-38920600	Strong transcription	Thymus	Thymus
37	chr2:38912400-38917600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:38912600-38920800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:38912600-38921000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:38912600-38932000	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:38912800-38917600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr2:38912800-38917600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:38912800-38917600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:38912800-38917600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:38912800-38924200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:38913200-38919200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:38913200-38919800	Weak transcription	Gastric	stomach
48	chr2:38913800-38938800	Weak transcription	Fetal Brain Male	brain
49	chr2:38914200-38919800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:38914400-38930000	Weak transcription	Left Ventricle	heart

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