Variant report

Variant	rs9871229
Chromosome Location	chr3:150938380-150938381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10513387	1.00[ASN][1000 genomes]
rs10513393	0.89[AFR][1000 genomes]
rs13321176	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13322794	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1549829	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1554120	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17204437	0.89[AFR][1000 genomes]
rs17290219	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17304673	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920393	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28386791	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28734805	0.80[EUR][1000 genomes]
rs28810515	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28831788	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55936523	0.87[AFR][1000 genomes]
rs6773020	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6780660	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6792089	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs722133	1.00[ASN][1000 genomes]
rs73155751	1.00[ASN][1000 genomes]
rs73155773	1.00[ASN][1000 genomes]
rs73155776	0.87[AFR][1000 genomes]
rs73157938	0.88[EUR][1000 genomes]
rs73157954	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7614811	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9812617	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9814936	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9817216	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818251	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9819885	0.84[EUR][1000 genomes]
rs9821749	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821937	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831242	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9836053	1.00[ASN][1000 genomes]
rs9838990	0.89[AFR][1000 genomes]
rs9840232	0.89[AFR][1000 genomes]
rs9841430	0.83[EUR][1000 genomes]
rs9850762	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9853676	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9854017	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854126	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9856118	0.89[AFR][1000 genomes]
rs9859854	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9868643	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9871624	0.90[EUR][1000 genomes]
rs9872645	0.89[AFR][1000 genomes]
rs9875587	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9876268	0.89[AFR][1000 genomes]
rs9880395	0.86[EUR][1000 genomes]
rs9881116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
2	chr3:150928800-150943800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:150928800-150946200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:150928800-150952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:150928800-150953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:150929000-150943200	Weak transcription	Psoas Muscle	Psoas
7	chr3:150929000-150945200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:150929200-150945400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:150929600-150939200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:150932200-150942800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:150932600-150946200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:150934600-150939000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:150935400-150939200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:150935400-150939800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:150935400-150946200	Weak transcription	Aorta	Aorta
16	chr3:150935600-150938600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:150935600-150944000	Weak transcription	Fetal Stomach	stomach
18	chr3:150935600-150945200	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:150935600-150945400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:150936200-150939200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:150936800-150939200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:150937000-150939200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:150937000-150942200	Weak transcription	Liver	Liver
24	chr3:150937200-150939200	Weak transcription	Primary B cells from cord blood	blood
25	chr3:150937400-150939000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:150937600-150939800	Weak transcription	NHLF	lung
27	chr3:150937600-150944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:150937600-150944200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:150937800-150945200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:150938000-150940200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr3:150938000-150940200	Weak transcription	Hela-S3	cervix
32	chr3:150938200-150938600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:150938200-150939800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:150938200-150940000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr3:150938200-150945800	Weak transcription	Fetal Heart	heart

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