Variant report

Variant	rs1599826
Chromosome Location	chr3:28284088-28284089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:28239745..28241981-chr3:28283804..28285570,2	K562	blood:
2	chr3:28281324..28283221-chr3:28283797..28285477,2	MCF-7	breast:
3	chr3:27809091..27811798-chr3:28283173..28285576,2	MCF-7	breast:
4	chr3:28282338..28284629-chr3:28303115..28305823,2	K562	blood:
5	chr3:28279814..28284603-chr3:28388127..28392296,9	K562	blood:
6	chr3:28283572..28286334-chr3:28300676..28304694,4	K562	blood:
7	chr3:28279814..28285757-chr3:28388127..28392208,14	K562	blood:

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction
ENSG00000163512	Chromatin interaction
ENSG00000206559	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11706332	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11708424	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11720107	0.92[CHB][hapmap]
rs11918050	0.83[CHB][hapmap]
rs11921692	0.92[CHB][hapmap]
rs11921943	0.92[CHB][hapmap]
rs12107256	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13081520	0.92[CHB][hapmap]
rs13082167	0.92[CHB][hapmap]
rs13083544	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085075	0.92[CHB][hapmap]
rs13085245	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13087143	0.92[CHB][hapmap]
rs13087774	0.92[CHB][hapmap]
rs13090296	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13090439	0.92[CHB][hapmap]
rs13092618	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13093242	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095628	0.92[CHB][hapmap]
rs13095675	0.92[CHB][hapmap]
rs13099152	0.83[ASN][1000 genomes]
rs1606386	0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1606388	0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1610238	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17021221	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17021306	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17021402	0.84[CHB][hapmap]
rs17357206	0.92[CHB][hapmap]
rs17638742	0.92[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs17638782	0.83[ASN][1000 genomes]
rs17638991	0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs17695765	0.92[CHB][hapmap]
rs17695884	0.92[CHB][hapmap]
rs17696025	0.92[CHB][hapmap]
rs1870259	0.92[CHB][hapmap]
rs2016948	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34017994	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34419916	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34541614	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34574968	0.82[ASN][1000 genomes]
rs34681294	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34748842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35217335	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35232922	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35439056	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35460328	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35496780	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35530532	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35565264	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35575798	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35678778	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35736614	0.83[ASN][1000 genomes]
rs35768817	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35845822	0.83[ASN][1000 genomes]
rs35937120	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36105900	0.92[CHB][hapmap]
rs3762797	0.92[CHB][hapmap]
rs4452283	0.92[CHB][hapmap]
rs4522735	0.83[ASN][1000 genomes]
rs4680909	0.92[CHB][hapmap]
rs4680913	0.92[CHB][hapmap]
rs56946005	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251105	0.82[ASN][1000 genomes]
rs62251108	0.84[ASN][1000 genomes]
rs62252069	0.83[ASN][1000 genomes]
rs66502736	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66716911	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67023418	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771057	0.92[CHB][hapmap]
rs6771460	0.92[CHB][hapmap]
rs68097246	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71087683	0.83[ASN][1000 genomes]
rs7434193	0.92[CHB][hapmap]
rs7635383	0.84[ASN][1000 genomes]
rs7639750	0.92[CHB][hapmap]
rs7641491	0.92[CHB][hapmap]
rs7649498	0.92[CHB][hapmap]
rs7651883	0.92[CHB][hapmap]
rs952888	0.81[ASN][1000 genomes]
rs9843464	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28282000-28284600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:28282200-28284200	Active TSS	Right Atrium	heart
3	chr3:28282200-28284400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:28282400-28284200	Active TSS	Psoas Muscle	Psoas
5	chr3:28282400-28284400	Active TSS	Colonic Mucosa	Colon
6	chr3:28282400-28284400	Active TSS	Fetal Brain Male	brain
7	chr3:28282600-28284200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:28282600-28284200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:28282600-28284200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:28282600-28284200	Active TSS	Fetal Stomach	stomach
11	chr3:28282600-28284200	Active TSS	NHLF	lung
12	chr3:28282600-28284400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:28282600-28284400	Active TSS	Brain Anterior Caudate	brain
14	chr3:28282600-28284400	Active TSS	Stomach Mucosa	stomach
15	chr3:28282600-28284600	Active TSS	A549	lung
16	chr3:28282800-28284200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:28282800-28284200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr3:28282800-28284200	Active TSS	HMEC	breast
19	chr3:28282800-28284400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr3:28282800-28284400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr3:28282800-28284400	Active TSS	Fetal Kidney	kidney
22	chr3:28282800-28284600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:28282800-28284600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:28282800-28284600	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr3:28283200-28284400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:28283400-28284200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr3:28283600-28284200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:28283600-28284200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr3:28283600-28284200	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr3:28283600-28284200	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr3:28283600-28284200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr3:28283600-28284200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr3:28283600-28284200	Flanking Active TSS	HUVEC	blood vessel
34	chr3:28283600-28284200	Flanking Active TSS	Osteobl	bone
35	chr3:28283600-28284400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:28283600-28284400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr3:28283600-28284400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:28283600-28284400	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr3:28283600-28284400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr3:28283600-28284400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:28283600-28284400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:28283600-28284600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr3:28283600-28284600	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr3:28283800-28284200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr3:28283800-28284200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr3:28283800-28284200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:28283800-28284200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:28283800-28284200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr3:28283800-28284200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:28283800-28284200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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