Variant report

Variant	rs9289138
Chromosome Location	chr3:119739297-119739298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1154596	0.84[ASN][1000 genomes]
rs1154597	0.84[ASN][1000 genomes]
rs11921053	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12494560	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13312998	0.84[ASN][1000 genomes]
rs13314595	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1579031	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16830689	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1719889	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs28516957	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs334535	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334536	0.96[EUR][1000 genomes]
rs334559	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334560	0.96[EUR][1000 genomes]
rs334566	0.96[EUR][1000 genomes]
rs3853592	0.84[ASN][1000 genomes]
rs4072520	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4450859	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs56126162	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58043853	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60272712	0.84[ASN][1000 genomes]
rs6438554	0.84[ASN][1000 genomes]
rs6438555	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66650215	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6762640	0.84[ASN][1000 genomes]
rs6769435	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770314	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771023	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774693	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775397	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6779828	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784239	0.84[ASN][1000 genomes]
rs6785050	0.84[ASN][1000 genomes]
rs6790751	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6795874	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802301	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6807868	0.84[ASN][1000 genomes]
rs7613197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617372	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7620750	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7635604	0.84[ASN][1000 genomes]
rs7636600	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7649661	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7652172	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs968824	0.96[EUR][1000 genomes]
rs9851174	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9859778	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9879992	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
2	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
3	chr3:119720200-119741000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:119723600-119740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:119724000-119741400	Weak transcription	Thymus	Thymus
6	chr3:119730000-119743000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:119730000-119743000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:119730600-119740800	Weak transcription	Left Ventricle	heart
9	chr3:119730600-119741600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:119731000-119741400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:119731400-119752400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:119731800-119739800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:119732000-119739400	Weak transcription	Ovary	ovary
14	chr3:119732200-119747200	Weak transcription	Gastric	stomach
15	chr3:119732200-119747600	Weak transcription	Right Ventricle	heart
16	chr3:119732600-119740800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:119732600-119741600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:119732600-119748400	Weak transcription	Brain Angular Gyrus	brain
19	chr3:119732600-119748600	Weak transcription	HSMM	muscle
20	chr3:119732600-119757800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:119732800-119746200	Weak transcription	Fetal Lung	lung
22	chr3:119732800-119749200	Weak transcription	Fetal Stomach	stomach
23	chr3:119733000-119747400	Weak transcription	Right Atrium	heart
24	chr3:119733200-119744200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:119733400-119741600	Weak transcription	Osteobl	bone
26	chr3:119733800-119739400	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:119734000-119739400	Weak transcription	Brain Substantia Nigra	brain
28	chr3:119734000-119740400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:119734200-119741000	Weak transcription	Primary T cells from cord blood	blood
30	chr3:119734800-119750000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:119735000-119739400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:119735000-119751600	Weak transcription	Primary B cells from cord blood	blood
33	chr3:119735200-119741000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:119735200-119742800	Weak transcription	Fetal Brain Female	brain
35	chr3:119735800-119744400	Weak transcription	HMEC	breast
36	chr3:119736000-119746400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:119736400-119739400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:119736600-119744000	Weak transcription	Fetal Intestine Small	intestine
39	chr3:119737000-119741400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:119737000-119749400	Weak transcription	Stomach Mucosa	stomach
41	chr3:119737000-119751800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr3:119737200-119739400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:119737200-119740200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:119737200-119740400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:119737400-119739400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:119737400-119739400	Weak transcription	Adipose Nuclei	Adipose
47	chr3:119737400-119739400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:119737400-119739800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:119737400-119739800	Weak transcription	Lung	lung
50	chr3:119737400-119739800	Weak transcription	Psoas Muscle	Psoas

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