Variant report

Variant	rs2872006
Chromosome Location	chr3:78663634-78663635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1027832	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1027833	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1507420	0.85[YRI][hapmap]
rs1507421	0.82[EUR][1000 genomes]
rs2872005	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3773195	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3821594	0.85[YRI][hapmap]
rs3821596	0.82[TSI][hapmap]
rs4680941	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681004	0.81[EUR][1000 genomes]
rs7614084	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877017	chr3:77881397-78670654	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv529995	chr3:78188643-78739698	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1010650	chr3:78505564-78699161	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78638600-78666800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:78638600-78676400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:78642400-78692600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:78646200-78683400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:78646800-78676400	Weak transcription	Lung	lung
6	chr3:78647200-78701000	Weak transcription	Spleen	Spleen
7	chr3:78647400-78694800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:78647600-78675600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:78648600-78686800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:78649400-78681200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:78650600-78666800	Weak transcription	Gastric	stomach
12	chr3:78651600-78666800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:78651600-78666800	Weak transcription	Esophagus	oesophagus
14	chr3:78652600-78684200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:78653600-78676200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:78653800-78682400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:78654000-78674800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:78654200-78675600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:78654200-78682400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:78654200-78696800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:78654200-78708800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:78654200-78746600	Weak transcription	NHDF-Ad	bronchial
23	chr3:78654600-78697000	Weak transcription	Osteobl	bone
24	chr3:78654800-78706800	Weak transcription	NHLF	lung
25	chr3:78654800-78711000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:78655200-78667000	Weak transcription	Left Ventricle	heart
27	chr3:78655400-78679800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:78655600-78678600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:78656000-78671800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:78656000-78673800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:78656000-78692800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:78656000-78718600	Weak transcription	Fetal Intestine Large	intestine
33	chr3:78656200-78665800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:78656200-78666400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:78656200-78675800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:78656200-78676400	Weak transcription	Brain Anterior Caudate	brain
37	chr3:78656200-78678000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:78656200-78678800	Weak transcription	Fetal Kidney	kidney
39	chr3:78656200-78684400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:78656200-78687800	Weak transcription	Primary T cells from cord blood	blood
41	chr3:78656200-78690800	Weak transcription	HMEC	breast
42	chr3:78656200-78711000	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:78656600-78666600	Weak transcription	Aorta	Aorta
44	chr3:78656600-78666600	Weak transcription	Fetal Stomach	stomach
45	chr3:78656800-78678800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:78659400-78704400	Weak transcription	Fetal Intestine Small	intestine
47	chr3:78659800-78676200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:78659800-78682400	Weak transcription	HSMMtube	muscle
49	chr3:78659800-78682400	Weak transcription	NHEK	skin
50	chr3:78660400-78676200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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