Variant report

Variant	rs9819398
Chromosome Location	chr3:78761585-78761586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10049014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10428105	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11914618	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11915745	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11917512	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11919682	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11920344	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11923747	0.83[ASN][1000 genomes]
rs11925970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11927666	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11928868	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12106862	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1395784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs1395785	0.83[CHB][hapmap]
rs1457659	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17016453	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17016466	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17303276	0.84[ASN][1000 genomes]
rs17375110	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17375496	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17375739	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1865861	0.82[CEU][hapmap]
rs1865863	0.83[CEU][hapmap]
rs2031051	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271151	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs28494803	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3732663	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3773220	0.83[CHB][hapmap]
rs3773224	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773225	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773226	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773227	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3773231	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773234	0.94[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3773239	0.91[ASN][1000 genomes]
rs3773240	0.89[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs3773245	0.91[ASN][1000 genomes]
rs3821601	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3821602	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821603	0.94[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs4263256	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58423115	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58561177	0.82[ASN][1000 genomes]
rs60568341	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61053911	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67137735	0.84[ASN][1000 genomes]
rs67347336	0.84[ASN][1000 genomes]
rs67498832	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6769933	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6787349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6788434	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6788511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6806079	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs716385	0.83[CHB][hapmap]
rs73109717	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73109772	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73109774	0.91[ASN][1000 genomes]
rs73850750	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7610686	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7613490	0.94[CEU][hapmap];0.94[JPT][hapmap]
rs7616495	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7622194	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7624482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7653782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs767182	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9309810	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9309811	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9309814	0.84[ASN][1000 genomes]
rs9808950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9823359	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9831098	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9840033	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9866912	0.82[CEU][hapmap]
rs9880072	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9880316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9882811	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9883582	0.87[EUR][1000 genomes]
rs997274	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][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	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
2	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1842222	chr3:78744206-78778901	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr3:78733800-78778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:78735200-78765600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:78740400-78773800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
5	chr3:78749000-78765800	Weak transcription	Ovary	ovary
6	chr3:78749600-78765600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:78752200-78773600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:78752600-78771000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:78753200-78765800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:78753600-78762400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:78754000-78762400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:78754000-78765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:78754000-78772200	Weak transcription	Brain Substantia Nigra	brain
15	chr3:78756200-78765800	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:78756200-78773800	Weak transcription	Fetal Kidney	kidney
17	chr3:78756800-78762200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:78756800-78777800	Weak transcription	Osteobl	bone
19	chr3:78757000-78762000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:78757000-78765600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:78757000-78771000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:78757200-78762600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:78757200-78765400	Weak transcription	Fetal Stomach	stomach
24	chr3:78757200-78765800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:78757200-78768400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:78757200-78773800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:78757200-78775000	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:78757400-78762600	Weak transcription	Fetal Lung	lung
29	chr3:78758600-78765800	Weak transcription	HepG2	liver
30	chr3:78761000-78762800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:78761200-78765800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:78761200-78777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:78761400-78763200	Enhancers	Primary T cells from cord blood	blood
34	chr3:78761400-78777400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:78761400-78777600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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