Variant report

Variant	rs12497227
Chromosome Location	chr3:143560530-143560531
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10433437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1394403	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs16854417	0.90[CHB][hapmap]
rs16854421	0.90[CHB][hapmap]
rs16854423	0.90[CHB][hapmap]
rs16854424	0.90[CHB][hapmap]
rs16854463	0.90[CHB][hapmap]
rs16854493	0.90[CHB][hapmap]
rs16854503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs16854525	0.90[CHB][hapmap]
rs1823220	0.90[CHB][hapmap]
rs1900643	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1989180	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2134913	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2361199	0.90[CHB][hapmap]
rs2361204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839613	1.00[CEU][hapmap]
rs4839614	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs4839659	0.90[CHB][hapmap]
rs4839660	0.90[CHB][hapmap]
rs4839661	0.90[CHB][hapmap]
rs4839663	0.90[CHB][hapmap]
rs4839670	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6763660	0.82[CHB][hapmap]
rs6764661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6765414	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs6769847	0.90[CHB][hapmap]
rs6776336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6792031	0.90[CHB][hapmap]
rs6804065	0.90[CHB][hapmap]
rs7621206	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7651412	0.90[CHB][hapmap];0.85[AMR][1000 genomes]
rs7652644	0.90[CHB][hapmap]
rs9822158	0.90[CHB][hapmap]
rs9827103	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9832471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9847107	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.93[ASN][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:143545600-143565400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:143549200-143565200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:143549400-143565000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143550000-143565200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:143551400-143561600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:143551400-143563000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:143551400-143565800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:143551800-143563600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:143554200-143565800	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:143555400-143564200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:143556800-143563800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:143558400-143561600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:143558400-143563800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:143558400-143566600	Weak transcription	Esophagus	oesophagus
16	chr3:143558600-143561200	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:143558600-143566000	Weak transcription	Ovary	ovary
18	chr3:143559000-143561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:143559600-143562400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:143559800-143561400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:143559800-143563600	Weak transcription	Primary B cells from cord blood	blood
22	chr3:143559800-143565800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:143559800-143566400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:143559800-143566400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:143560000-143561000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:143560200-143560600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:143560200-143561200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:143560200-143561400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:143560200-143561400	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:143560200-143561400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:143560200-143563200	Weak transcription	Brain Substantia Nigra	brain
32	chr3:143560200-143563200	Weak transcription	GM12878-XiMat	blood
33	chr3:143560200-143563800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:143560200-143564000	Weak transcription	Fetal Lung	lung
35	chr3:143560200-143564400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:143560200-143565200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:143560200-143565800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:143560200-143566600	Weak transcription	Small Intestine	intestine

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