Variant report

Variant	rs303884
Chromosome Location	chr6:25062467-25062468
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	chr6:25060649..25063407-chr6:25066068..25067636,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12524842	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12525328	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12525405	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12528227	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12661796	0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12663160	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12665174	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13195161	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13196712	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13203073	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209444	0.91[EUR][1000 genomes]
rs13218879	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562422	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562423	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1597010	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1597011	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1597012	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs160034	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900551	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923192	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923193	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs192773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273671	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs302992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34322558	0.92[EUR][1000 genomes]
rs34475409	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34693126	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35028017	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35553146	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36030790	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36078207	0.91[EUR][1000 genomes]
rs3792974	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs3792983	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs3812109	0.81[CEU][hapmap]
rs4711071	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4711072	0.86[ASN][1000 genomes]
rs4711073	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4711075	0.91[EUR][1000 genomes]
rs4712882	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs56108659	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67240854	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67795839	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67927735	0.92[EUR][1000 genomes]
rs72826363	0.84[EUR][1000 genomes]
rs7738141	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs895676	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25055400-25064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:25057600-25080400	Weak transcription	Thymus	Thymus
3	chr6:25057800-25062800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:25057800-25062800	Weak transcription	Placenta	Placenta
5	chr6:25059600-25062600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:25060400-25063000	Enhancers	Adipose Nuclei	Adipose
7	chr6:25061200-25063200	Enhancers	NHDF-Ad	bronchial
8	chr6:25061200-25065200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:25061400-25062800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:25061400-25062800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:25061400-25062800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:25061400-25062800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:25061400-25063000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:25061400-25063000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:25061400-25063000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:25061400-25063000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:25061400-25063200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:25061400-25063200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:25061400-25063200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:25061400-25063200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:25061400-25063200	Enhancers	Fetal Muscle Leg	muscle
22	chr6:25061400-25063400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:25061400-25063600	Enhancers	Fetal Heart	heart
24	chr6:25061400-25065000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:25061600-25062800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:25061600-25063000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:25061600-25063000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:25061600-25063000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:25061600-25063200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr6:25061600-25063200	Enhancers	Ovary	ovary
31	chr6:25061800-25062800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:25061800-25062800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:25061800-25063000	Weak transcription	Left Ventricle	heart
34	chr6:25061800-25063200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr6:25061800-25063200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr6:25061800-25066000	Weak transcription	HSMMtube	muscle
37	chr6:25062000-25062600	Enhancers	H9 Cell Line	embryonic stem cell
38	chr6:25062000-25062800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:25062000-25063000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:25062200-25063000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:25062200-25063000	Enhancers	Osteobl	bone
42	chr6:25062200-25063800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:25062400-25062600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:25062400-25062800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:25062400-25062800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr6:25062400-25063000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:25062400-25063400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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