Variant report

Variant	rs3112148
Chromosome Location	chr2:39051180-39051181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39003837..39006162-chr2:39050113..39052054,2	MCF-7	breast:
2	chr2:38976908..38981867-chr2:39050395..39056507,16	K562	blood:
3	chr2:38976340..38977932-chr2:39049714..39052314,2	K562	blood:
4	chr2:39045661..39047952-chr2:39049221..39051598,2	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10165289	1.00[EUR][1000 genomes]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10180775	1.00[EUR][1000 genomes]
rs10186448	1.00[EUR][1000 genomes]
rs10186842	1.00[EUR][1000 genomes]
rs10194533	1.00[EUR][1000 genomes]
rs10202876	1.00[EUR][1000 genomes]
rs10495882	1.00[EUR][1000 genomes]
rs12329307	1.00[EUR][1000 genomes]
rs13382974	1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13396461	1.00[EUR][1000 genomes]
rs13399254	1.00[EUR][1000 genomes]
rs13409776	1.00[EUR][1000 genomes]
rs13420732	1.00[EUR][1000 genomes]
rs13421894	1.00[EUR][1000 genomes]
rs1451278	1.00[EUR][1000 genomes]
rs17023037	1.00[EUR][1000 genomes]
rs17023042	1.00[EUR][1000 genomes]
rs17023045	1.00[EUR][1000 genomes]
rs17023148	1.00[EUR][1000 genomes]
rs17023149	1.00[EUR][1000 genomes]
rs17023214	1.00[EUR][1000 genomes]
rs17023241	1.00[EUR][1000 genomes]
rs17425982	1.00[EUR][1000 genomes]
rs1901290	1.00[EUR][1000 genomes]
rs2218850	1.00[EUR][1000 genomes]
rs2373466	1.00[EUR][1000 genomes]
rs2373472	1.00[EUR][1000 genomes]
rs28473018	1.00[EUR][1000 genomes]
rs28499207	1.00[EUR][1000 genomes]
rs3099938	1.00[EUR][1000 genomes]
rs3099953	1.00[EUR][1000 genomes]
rs3099973	1.00[EUR][1000 genomes]
rs3099976	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3099983	0.81[AFR][1000 genomes]
rs3099986	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3099996	1.00[EUR][1000 genomes]
rs3099997	1.00[EUR][1000 genomes]
rs3112145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112146	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112155	1.00[EUR][1000 genomes]
rs3112157	1.00[EUR][1000 genomes]
rs3112158	1.00[EUR][1000 genomes]
rs3112160	1.00[EUR][1000 genomes]
rs3112164	1.00[EUR][1000 genomes]
rs3112174	1.00[EUR][1000 genomes]
rs3112177	1.00[EUR][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs7565814	1.00[EUR][1000 genomes]
rs7599990	1.00[EUR][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	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39009200-39052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
5	chr2:39024000-39053000	Weak transcription	Psoas Muscle	Psoas
6	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
8	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:39033000-39053000	Weak transcription	Fetal Brain Male	brain
10	chr2:39036000-39054000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:39036400-39051600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:39037400-39052000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:39037400-39054000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:39037400-39054000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:39037400-39054600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:39037800-39053800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:39038200-39056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:39038800-39102200	Weak transcription	Gastric	stomach
21	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
23	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
25	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
26	chr2:39040600-39056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:39040800-39054200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:39042800-39063000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
30	chr2:39043200-39051200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:39043200-39052600	Weak transcription	Aorta	Aorta
32	chr2:39043400-39053000	Weak transcription	Brain Substantia Nigra	brain
33	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
34	chr2:39043800-39053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:39043800-39053800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:39044800-39056800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:39045800-39052800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:39046000-39051400	Weak transcription	GM12878-XiMat	blood
39	chr2:39046000-39052600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:39046000-39052600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:39046000-39053000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:39046000-39073200	Weak transcription	Pancreas	Pancrea
43	chr2:39046200-39051200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:39046200-39052600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:39046200-39070200	Weak transcription	NHLF	lung
46	chr2:39046400-39057200	Weak transcription	HepG2	liver
47	chr2:39046800-39053000	Weak transcription	Lung	lung
48	chr2:39046800-39053200	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:39048000-39055600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:39048400-39054200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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