Variant report

Variant	rs12430086
Chromosome Location	chr13:39590026-39590027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:39588378..39591608-chr13:39610325..39612759,3	MCF-7	breast:
2	chr13:39581567..39584670-chr13:39588176..39591409,3	K562	blood:
3	chr13:39589682..39591724-chr13:39593267..39594841,2	K562	blood:
4	chr13:39581808..39584670-chr13:39588176..39590668,3	K562	blood:
5	chr13:39582312..39584090-chr13:39587893..39590374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11840611	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12857215	0.83[ASN][1000 genomes]
rs1326404	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1409442	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536342	0.83[EUR][1000 genomes]
rs1887107	0.84[ASN][1000 genomes]
rs1887111	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1926474	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1926475	0.85[ASN][1000 genomes]
rs2094251	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2324160	0.85[ASN][1000 genomes]
rs3751376	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3865000	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6563660	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6563661	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[ASN][1000 genomes]
rs6563662	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6563663	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67948555	0.91[ASN][1000 genomes]
rs71439792	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7324256	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7324837	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7325996	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7337269	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7489497	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7985641	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7995325	0.85[ASN][1000 genomes]
rs9315647	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs9315649	0.85[ASN][1000 genomes]
rs9315650	0.83[EUR][1000 genomes]
rs9566395	0.85[ASN][1000 genomes]
rs9576671	0.89[ASN][1000 genomes]
rs9576672	0.91[ASN][1000 genomes]
rs9576680	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576687	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9576720	0.85[ASN][1000 genomes]
rs9576723	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9594319	0.85[ASN][1000 genomes]
rs9603500	0.85[ASN][1000 genomes]
rs9603503	0.83[EUR][1000 genomes]
rs9888511	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39581600-39590800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:39581600-39592000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr13:39581600-39592400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:39581800-39592200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:39581800-39593200	Strong transcription	HSMM	muscle
6	chr13:39581800-39597000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr13:39582000-39596600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr13:39582000-39608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:39582200-39590800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:39582200-39592600	Strong transcription	Fetal Thymus	thymus
11	chr13:39582200-39593400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr13:39582200-39596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr13:39582200-39596800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr13:39582200-39597400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr13:39582400-39590400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr13:39582400-39590400	Strong transcription	GM12878-XiMat	blood
17	chr13:39582400-39605400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr13:39582600-39592000	Strong transcription	Placenta	Placenta
19	chr13:39582600-39592400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr13:39582600-39592400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr13:39582800-39593600	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr13:39583000-39592400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:39583200-39592400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:39583200-39592400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr13:39583200-39592400	Strong transcription	Adipose Nuclei	Adipose
26	chr13:39583200-39593200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:39583200-39606600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr13:39583400-39592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr13:39583400-39592600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr13:39583400-39593200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr13:39583600-39597200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr13:39583800-39592400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr13:39583800-39592600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr13:39584000-39597600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr13:39584200-39591200	Strong transcription	NHLF	lung
36	chr13:39584200-39591400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr13:39584200-39592400	Strong transcription	Osteobl	bone
38	chr13:39584400-39590800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:39584400-39591400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr13:39584400-39592400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr13:39584400-39592400	Strong transcription	Dnd41	blood
42	chr13:39584400-39592600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr13:39584400-39593000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr13:39584400-39593200	Strong transcription	Fetal Kidney	kidney
45	chr13:39584600-39591000	Strong transcription	Fetal Brain Female	brain
46	chr13:39584600-39591400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:39584600-39591400	Strong transcription	HMEC	breast
48	chr13:39584600-39591600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr13:39584600-39592400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr13:39584600-39592400	Strong transcription	Left Ventricle	heart

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