Variant report

Variant	rs9461081
Chromosome Location	chr6:24929488-24929489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24929367..24931167-chr6:24936238..24937978,2	MCF-7	breast:
2	chr6:24928799..24930650-chr6:24931112..24934002,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11760083	0.94[CHB][hapmap];0.96[CHD][hapmap]
rs1410684	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889798	0.94[CHB][hapmap]
rs587009	0.83[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6929465	0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6929680	0.88[ASN][1000 genomes]
rs9461082	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467355	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3422272	chr6:24925373-24929771	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9461081	PGBD1	cis	cerebellum	SCAN
rs9461081	SCGN	cis	cerebellum	SCAN
rs9461081	HIST1H2BF	cis	cerebellum	SCAN
rs9461081	HIST1H3C	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24919200-24930600	Weak transcription	Gastric	stomach
2	chr6:24920600-24930000	Weak transcription	Right Atrium	heart
3	chr6:24920600-24932000	Weak transcription	Fetal Kidney	kidney
4	chr6:24921200-24929600	Weak transcription	Psoas Muscle	Psoas
5	chr6:24924400-24930000	Enhancers	Hela-S3	cervix
6	chr6:24924600-24930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:24924600-24930600	Weak transcription	Spleen	Spleen
8	chr6:24924600-24930800	Weak transcription	Brain Germinal Matrix	brain
9	chr6:24925000-24930800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:24925400-24930600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:24925600-24930600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:24925600-24930600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:24925600-24931000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:24925600-24931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:24925600-24931800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:24926200-24930800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:24926800-24931600	Weak transcription	Stomach Mucosa	stomach
18	chr6:24926800-24934400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
19	chr6:24927000-24929600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:24927000-24930600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:24927000-24930600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:24927000-24930800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:24927000-24931600	Weak transcription	Fetal Intestine Small	intestine
24	chr6:24927200-24933600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
25	chr6:24927400-24931800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:24927400-24932200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
27	chr6:24927600-24929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:24927600-24931600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:24927600-24932400	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
30	chr6:24927800-24929600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:24927800-24929600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:24927800-24930600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:24927800-24931400	Enhancers	Osteobl	bone
34	chr6:24927800-24932800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:24927800-24933200	Enhancers	HSMM	muscle
36	chr6:24927800-24934400	Enhancers	HSMMtube	muscle
37	chr6:24928000-24929600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr6:24928000-24930600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:24928000-24931600	Genic enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:24928000-24933400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:24928000-24934200	Enhancers	Fetal Lung	lung
42	chr6:24928200-24930800	Enhancers	Fetal Thymus	thymus
43	chr6:24928200-24931800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:24928200-24933000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:24928400-24930600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:24928400-24932600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr6:24928400-24933000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:24928400-24933400	Enhancers	Fetal Heart	heart
49	chr6:24928600-24930400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:24928800-24929600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood

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