Variant report

Variant	rs1539002
Chromosome Location	chr6:4934858-4934859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4932165..4934498-chr6:4934564..4936978,2	MCF-7	breast:
2	chr6:4934856..4938294-chr6:4940217..4942355,4	K562	blood:
3	chr6:4928518..4932053-chr6:4933158..4936712,4	K562	blood:
4	chr6:4932686..4935166-chr6:4938029..4940915,3	MCF-7	breast:
5	chr6:4932719..4935365-chr6:5002705..5005328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124787	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1112267	0.87[JPT][hapmap]
rs13208366	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1341093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1341094	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1539003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2027418	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2039906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2039907	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804547	0.83[EUR][1000 genomes]
rs6911199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6911937	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6922170	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7743681	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9378921	0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9392642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4908000-4935600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr6:4911000-4935200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr6:4913200-4936000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:4913200-4941000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:4913600-4938000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:4915800-4942400	Weak transcription	Aorta	Aorta
7	chr6:4916600-4935400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:4917200-4935000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:4918000-4936000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:4923000-4937800	Weak transcription	Primary T cells from cord blood	blood
11	chr6:4925600-4941600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:4927600-4940200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:4928800-4935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:4929400-4941600	Weak transcription	Osteobl	bone
15	chr6:4930200-4939800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:4930800-4936000	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:4930800-4940200	Weak transcription	NH-A	brain
18	chr6:4930800-4940600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:4931200-4935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:4931600-4935000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:4932000-4942000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:4932200-4935800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:4932200-4935800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:4932200-4940800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:4932200-4945000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:4932400-4935600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:4932400-4935600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:4932400-4935800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:4932400-4936000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:4932400-4936200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:4932400-4936600	Weak transcription	Brain Anterior Caudate	brain
32	chr6:4932400-4936800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:4932400-4936800	Weak transcription	NHLF	lung
34	chr6:4932400-4941000	Weak transcription	HSMM	muscle
35	chr6:4932400-4941400	Weak transcription	NHDF-Ad	bronchial
36	chr6:4932400-4941600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:4932400-4942000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:4932400-4942400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:4932600-4935000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:4932600-4935200	Weak transcription	HepG2	liver
41	chr6:4932600-4936200	Weak transcription	Fetal Heart	heart
42	chr6:4932600-4936400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:4932600-4936600	Weak transcription	Stomach Mucosa	stomach
44	chr6:4932600-4940600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:4932600-4941000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:4932600-4942200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:4932600-4944200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:4932600-4944600	Weak transcription	Colonic Mucosa	Colon
49	chr6:4932800-4936200	Weak transcription	A549	lung
50	chr6:4932800-4944400	Weak transcription	Thymus	Thymus

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