Variant report

Variant	rs3099938
Chromosome Location	chr2:39093401-39093402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39060039..39062647-chr2:39091366..39093415,2	K562	blood:
2	chr2:39089505..39093700-chr2:39094409..39098372,5	K562	blood:
3	chr2:39088675..39091170-chr2:39093044..39095216,2	MCF-7	breast:
4	chr2:39092323..39097069-chr2:39100019..39103136,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225284	Chromatin interaction
ENSG00000188010	Chromatin interaction
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10165289	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10186448	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10186842	1.00[CEU][hapmap];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]
rs13407659	1.00[EUR][1000 genomes]
rs13409776	1.00[EUR][1000 genomes]
rs13420732	1.00[EUR][1000 genomes]
rs13421894	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1451278	1.00[CEU][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17023037	1.00[EUR][1000 genomes]
rs17023042	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023045	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023148	1.00[EUR][1000 genomes]
rs17023149	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023214	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023241	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023292	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17425982	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1901290	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2044853	0.93[AFR][1000 genomes]
rs2218850	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2373466	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373472	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs28473018	1.00[EUR][1000 genomes]
rs28499207	1.00[EUR][1000 genomes]
rs3099947	1.00[CEU][hapmap]
rs3099953	1.00[EUR][1000 genomes]
rs3099973	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs3099986	1.00[EUR][1000 genomes]
rs3099996	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3099997	1.00[EUR][1000 genomes]
rs3112145	1.00[EUR][1000 genomes]
rs3112146	1.00[EUR][1000 genomes]
rs3112148	1.00[EUR][1000 genomes]
rs3112155	1.00[EUR][1000 genomes]
rs3112157	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112158	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112160	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112164	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112169	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3112174	1.00[EUR][1000 genomes]
rs3112176	1.00[CEU][hapmap]
rs3112177	1.00[EUR][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs6734212	1.00[EUR][1000 genomes]
rs6737680	1.00[EUR][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6754613	1.00[EUR][1000 genomes]
rs718312	1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7565814	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7583010	1.00[CEU][hapmap]
rs7599990	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9646968	1.00[EUR][1000 genomes]
rs9678084	1.00[CEU][hapmap]

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	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:39038800-39102200	Weak transcription	Gastric	stomach
3	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
5	chr2:39072200-39095400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:39080000-39102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:39081200-39102200	Weak transcription	Right Ventricle	heart
8	chr2:39081200-39102200	Weak transcription	Spleen	Spleen
9	chr2:39081200-39102400	Weak transcription	Pancreas	Pancrea
10	chr2:39086000-39094400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:39086400-39101800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:39087600-39095400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:39088200-39102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:39089200-39101800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:39089200-39101800	Weak transcription	Fetal Heart	heart
16	chr2:39089400-39094000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:39089400-39094200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:39089400-39094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:39089400-39095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:39089400-39101200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:39089400-39102000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:39089400-39102200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:39089400-39102200	Weak transcription	Ovary	ovary
24	chr2:39089400-39102200	Weak transcription	Small Intestine	intestine
25	chr2:39089600-39093800	Weak transcription	Fetal Stomach	stomach
26	chr2:39089600-39094000	Weak transcription	Thymus	Thymus
27	chr2:39089600-39094000	Weak transcription	Hela-S3	cervix
28	chr2:39089600-39094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:39089600-39101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:39089600-39102000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:39089600-39102000	Weak transcription	NHLF	lung
32	chr2:39089600-39102400	Weak transcription	Lung	lung
33	chr2:39089800-39097200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:39089800-39101800	Weak transcription	Brain Substantia Nigra	brain
35	chr2:39090000-39094200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:39090000-39102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:39090000-39102000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:39090200-39094600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:39090200-39101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:39090200-39102400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:39090400-39093600	Weak transcription	Fetal Thymus	thymus
42	chr2:39090400-39093800	Weak transcription	Brain Angular Gyrus	brain
43	chr2:39090400-39099400	Weak transcription	K562	blood
44	chr2:39090600-39093600	Weak transcription	HepG2	liver
45	chr2:39090600-39093800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:39090600-39094000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:39090600-39094200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:39090600-39094200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:39090600-39097200	Weak transcription	Brain Anterior Caudate	brain
50	chr2:39090600-39101800	Weak transcription	HUVEC	blood vessel

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