Variant report

Variant	rs1550509
Chromosome Location	chr3:143290692-143290693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10935498	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11707194	0.88[CEU][hapmap];0.81[CHB][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12494880	0.82[CHD][hapmap]
rs34224721	0.84[CEU][hapmap];0.81[CHB][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34973048	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4839645	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6771556	0.84[CEU][hapmap];0.81[CHB][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs727114	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143256000-143305600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:143270600-143304800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:143277400-143292400	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:143277400-143301200	Weak transcription	Esophagus	oesophagus
5	chr3:143277400-143303600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:143277400-143310200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:143277600-143292400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:143279000-143296200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:143281400-143292200	Weak transcription	Primary T cells from cord blood	blood
10	chr3:143284000-143306400	Weak transcription	Spleen	Spleen
11	chr3:143284400-143292600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:143284400-143299200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:143285000-143300400	Weak transcription	Brain Anterior Caudate	brain
14	chr3:143285200-143292200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:143285400-143290800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:143285600-143296200	Weak transcription	Primary B cells from cord blood	blood
17	chr3:143286800-143295600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:143286800-143298000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:143286800-143300400	Weak transcription	GM12878-XiMat	blood
20	chr3:143286800-143302000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:143286800-143304400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:143286800-143304800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:143287000-143297600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:143287000-143305000	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:143287200-143297400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:143287400-143295800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:143287400-143304800	Weak transcription	Fetal Intestine Small	intestine
28	chr3:143287600-143292800	Weak transcription	HUVEC	blood vessel
29	chr3:143289200-143291600	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:143289200-143292200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:143289400-143303000	Weak transcription	Fetal Stomach	stomach
32	chr3:143289600-143304600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:143289800-143291200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:143289800-143295200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:143290000-143291000	Enhancers	HSMMtube	muscle
36	chr3:143290000-143291200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:143290200-143290800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:143290200-143291000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr3:143290200-143291200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:143290200-143291200	Enhancers	HSMM	muscle
41	chr3:143290400-143291000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:143290400-143291000	Enhancers	Adipose Nuclei	Adipose
43	chr3:143290400-143291400	Strong transcription	Fetal Lung	lung
44	chr3:143290400-143295000	Weak transcription	Ovary	ovary
45	chr3:143290600-143290800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:143290600-143291000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr3:143290600-143291000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:143290600-143291000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:143290600-143291000	Enhancers	Osteobl	bone
50	chr3:143290600-143302400	Weak transcription	Stomach Smooth Muscle	stomach

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