Variant report

Variant	rs12995468
Chromosome Location	chr2:74266778-74266779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74262372..74265122-chr2:74265413..74267143,2	K562	blood:
2	chr2:74210143..74212604-chr2:74265569..74267635,2	MCF-7	breast:
3	chr2:74257577..74261263-chr2:74266569..74269691,3	K562	blood:
4	chr2:74266580..74268574-chr2:74271359..74274242,2	MCF-7	breast:
5	chr2:74263750..74267356-chr2:74281436..74283825,3	K562	blood:
6	chr2:74265210..74267434-chr2:74684359..74686371,2	MCF-7	breast:
7	chr2:74263852..74266331-chr2:74266668..74270220,4	K562	blood:

Variant related genes	Relation type
ENSG00000239779	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000187605	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10164943	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10168249	0.86[EUR][1000 genomes]
rs10168408	0.86[EUR][1000 genomes]
rs10168410	0.92[EUR][1000 genomes]
rs10179967	0.90[EUR][1000 genomes]
rs10188058	1.00[CHB][hapmap]
rs10191539	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10200470	0.92[EUR][1000 genomes]
rs1025424	1.00[CHB][hapmap]
rs11126424	0.88[EUR][1000 genomes]
rs11683738	1.00[CHB][hapmap]
rs11884748	0.86[EUR][1000 genomes]
rs11885172	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11886928	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11898903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328927	0.91[EUR][1000 genomes]
rs12713803	0.82[EUR][1000 genomes]
rs12713804	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs12713805	0.85[EUR][1000 genomes]
rs12713806	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12713808	0.92[EUR][1000 genomes]
rs12713809	0.90[EUR][1000 genomes]
rs12713810	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs12988533	0.84[EUR][1000 genomes]
rs12991192	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13005103	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006301	0.92[EUR][1000 genomes]
rs13006407	0.94[EUR][1000 genomes]
rs13011961	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013211	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014576	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs13016198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019449	1.00[ASN][1000 genomes]
rs13021880	0.91[EUR][1000 genomes]
rs13027288	0.90[EUR][1000 genomes]
rs13027623	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030414	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13387010	0.92[EUR][1000 genomes]
rs17404009	1.00[CHB][hapmap]
rs17676291	1.00[CHB][hapmap]
rs17725971	1.00[CHB][hapmap]
rs28450901	0.89[EUR][1000 genomes]
rs34136450	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34201525	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35592918	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35609589	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3902790	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4073048	0.90[EUR][1000 genomes]
rs4241260	0.92[EUR][1000 genomes]
rs4270374	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328662	0.86[EUR][1000 genomes]
rs4331526	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4364046	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4371381	0.88[EUR][1000 genomes]
rs4374402	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416242	0.92[EUR][1000 genomes]
rs4422181	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574138	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4578887	0.83[EUR][1000 genomes]
rs4621184	0.91[EUR][1000 genomes]
rs4852326	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4853003	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4853005	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4853006	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4853007	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4853009	0.92[EUR][1000 genomes]
rs60279245	0.89[EUR][1000 genomes]
rs6546884	0.84[EUR][1000 genomes]
rs6546885	0.86[EUR][1000 genomes]
rs6546886	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6546887	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6706327	0.92[EUR][1000 genomes]
rs6712566	1.00[ASN][1000 genomes]
rs6713313	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6714186	0.85[EUR][1000 genomes]
rs6717896	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741544	0.91[EUR][1000 genomes]
rs6743073	0.85[EUR][1000 genomes]
rs6745236	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6745576	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6745792	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6754218	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755711	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6756474	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs71337722	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71406850	1.00[ASN][1000 genomes]
rs7560668	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7584777	0.90[EUR][1000 genomes]
rs7587991	0.89[EUR][1000 genomes]
rs7589915	0.91[EUR][1000 genomes]
rs7592749	0.89[EUR][1000 genomes]
rs7593050	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597388	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601526	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7606491	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs870722	1.00[CHB][hapmap]
rs9309478	0.95[CEU][hapmap];0.90[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	esv3584956	chr2:74197109-74317135	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv818048	chr2:74225434-74313080	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 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	chr2:74231600-74273800	Weak transcription	A549	lung
2	chr2:74240000-74276200	Weak transcription	Hela-S3	cervix
3	chr2:74256000-74269600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:74259400-74269600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:74259800-74269200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:74260000-74267400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:74260000-74269400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:74260000-74269400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr2:74260000-74269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:74260000-74269800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:74260000-74269800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:74260000-74273200	Weak transcription	Brain Germinal Matrix	brain
13	chr2:74260200-74267000	Weak transcription	Fetal Heart	heart
14	chr2:74260200-74269200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:74260200-74270400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:74260200-74271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:74260200-74272600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:74260200-74273600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:74260400-74267000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:74260400-74270200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:74260400-74271600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:74260800-74270000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:74260800-74278400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:74262600-74267000	Enhancers	Thymus	Thymus
25	chr2:74262800-74267000	Enhancers	Primary B cells from peripheral blood	blood
26	chr2:74262800-74269400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:74263000-74269000	Enhancers	Fetal Thymus	thymus
28	chr2:74263000-74269800	Enhancers	Primary T cells from cord blood	blood
29	chr2:74263000-74270600	Enhancers	Placenta	Placenta
30	chr2:74263400-74267800	Enhancers	Brain Hippocampus Middle	brain
31	chr2:74264000-74268600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr2:74264000-74269400	Enhancers	Fetal Muscle Leg	muscle
33	chr2:74264200-74266800	Enhancers	Lung	lung
34	chr2:74264200-74269600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:74264400-74268600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:74264400-74270200	Weak transcription	Gastric	stomach
37	chr2:74264600-74269400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:74264600-74269400	Enhancers	Primary hematopoietic stem cells	blood
39	chr2:74264600-74269600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:74264600-74271400	Weak transcription	Brain Anterior Caudate	brain
41	chr2:74264600-74273800	Weak transcription	Colonic Mucosa	Colon
42	chr2:74264800-74267200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:74264800-74272200	Weak transcription	NHEK	skin
44	chr2:74264800-74311000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:74265000-74267400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:74265000-74267400	Weak transcription	Stomach Mucosa	stomach
47	chr2:74265000-74270200	Weak transcription	Fetal Lung	lung
48	chr2:74265000-74272600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:74265000-74272600	Weak transcription	Fetal Stomach	stomach
50	chr2:74265000-74272600	Weak transcription	Placenta Amnion	Placenta Amnion

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