Variant report

Variant	rs3099986
Chromosome Location	chr2:39056918-39056919
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39053503..39057037-chr2:39058758..39062643,3	K562	blood:
2	chr2:38974988..38979943-chr2:39053736..39058253,10	K562	blood:
3	chr2:38976872..38979840-chr2:39056753..39060826,5	K562	blood:
4	chr2:39055729..39058669-chr2:39100987..39103222,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188010	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

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]
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]
rs3112148	0.92[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]
rs6737680	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]
rs7602168	0.82[AFR][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	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
4	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
6	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:39038800-39102200	Weak transcription	Gastric	stomach
9	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
11	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
13	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:39042800-39063000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
16	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
17	chr2:39046000-39073200	Weak transcription	Pancreas	Pancrea
18	chr2:39046200-39070200	Weak transcription	NHLF	lung
19	chr2:39046400-39057200	Weak transcription	HepG2	liver
20	chr2:39048400-39060800	Strong transcription	Fetal Stomach	stomach
21	chr2:39050400-39062800	Weak transcription	Thymus	Thymus
22	chr2:39050400-39063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:39050400-39072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:39050400-39079800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:39050400-39079800	Weak transcription	Spleen	Spleen
26	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:39051000-39068600	Weak transcription	HMEC	breast
28	chr2:39052000-39061800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:39052200-39068600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:39053000-39057200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:39053200-39068600	Weak transcription	Brain Substantia Nigra	brain
32	chr2:39053200-39069600	Weak transcription	HUVEC	blood vessel
33	chr2:39053600-39057400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:39053600-39060000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:39053600-39062400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:39053800-39057200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:39053800-39057200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:39053800-39057200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:39053800-39057800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:39053800-39057800	Weak transcription	Brain Anterior Caudate	brain
41	chr2:39053800-39060600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:39053800-39060600	Weak transcription	Fetal Kidney	kidney
43	chr2:39053800-39061800	Weak transcription	Fetal Lung	lung
44	chr2:39053800-39062400	Weak transcription	Left Ventricle	heart
45	chr2:39053800-39062800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:39053800-39063000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:39053800-39063800	Weak transcription	Liver	Liver
48	chr2:39053800-39064600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:39053800-39068200	Weak transcription	HSMM	muscle
50	chr2:39053800-39068400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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