Variant report

Variant	rs3821602
Chromosome Location	chr3:78773470-78773471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78772880..78774546-chr3:78776083..78778103,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10049014	0.91[CHB][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10049102	0.93[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10428105	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs11914618	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11917512	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11919682	0.87[ASN][1000 genomes]
rs11920344	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11925970	0.92[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs11927666	0.81[ASN][1000 genomes]
rs11928868	0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12106862	0.81[ASN][1000 genomes]
rs1395784	0.86[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1457659	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17016453	0.81[ASN][1000 genomes]
rs17016466	0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17303276	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17375110	0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17375496	0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17375739	0.92[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1865860	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1865861	0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1865863	0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1961636	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2271151	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs28494803	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732663	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3773226	0.86[CHB][hapmap]
rs3773227	0.81[ASN][1000 genomes]
rs3773231	0.92[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773234	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773239	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773240	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773245	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821601	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3821603	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4263256	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4681013	0.81[JPT][hapmap]
rs56077922	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58423115	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61053911	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6548595	0.87[JPT][hapmap]
rs67137735	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67347336	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67498832	0.81[ASN][1000 genomes]
rs6769933	0.92[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6787349	0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6788434	0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6788511	0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6806079	0.81[ASN][1000 genomes]
rs73109717	0.81[ASN][1000 genomes]
rs73109772	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73109774	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73850750	0.81[ASN][1000 genomes]
rs7610686	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7616495	0.86[CHB][hapmap]
rs7622194	0.93[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7624482	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs7653782	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs767182	0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9309814	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9808950	0.93[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9819398	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9823359	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9840033	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9861603	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9866912	0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9880072	0.85[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880316	0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9882811	0.93[CHB][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997274	0.81[JPT][hapmap]

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	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
2	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
3	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:49 , 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	chr3:78740400-78773800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
4	chr3:78752200-78773600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:78756200-78773800	Weak transcription	Fetal Kidney	kidney
7	chr3:78756800-78777800	Weak transcription	Osteobl	bone
8	chr3:78757200-78773800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:78757200-78775000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:78761200-78777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:78761400-78777400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:78761400-78777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:78762800-78774000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:78763600-78773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:78764200-78777400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:78765800-78778000	Weak transcription	HMEC	breast
17	chr3:78766400-78774000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:78766400-78777400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:78766400-78778000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:78766400-78778000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:78766600-78773600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:78766600-78773800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:78766600-78773800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:78766600-78773800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:78766600-78774200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:78766600-78774200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:78766600-78778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:78766600-78778000	Weak transcription	Ovary	ovary
29	chr3:78766600-78783000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:78771000-78774600	Enhancers	Fetal Lung	lung
31	chr3:78771200-78774200	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:78771400-78773600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:78771400-78773800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:78771600-78774000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:78771600-78774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:78771800-78774200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:78772000-78774000	Weak transcription	A549	lung
38	chr3:78772000-78778000	Weak transcription	NHEK	skin
39	chr3:78772000-78792200	Weak transcription	HepG2	liver
40	chr3:78772200-78774400	Enhancers	Fetal Stomach	stomach
41	chr3:78772400-78774000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:78772800-78773800	Enhancers	Fetal Brain Male	brain
43	chr3:78772800-78776000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:78773000-78775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:78773200-78773600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:78773200-78775000	Weak transcription	Brain Anterior Caudate	brain
47	chr3:78773400-78773800	Weak transcription	Primary T cells from cord blood	blood
48	chr3:78773400-78773800	Active TSS	Brain Substantia Nigra	brain
49	chr3:78773400-78776200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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