Variant report

Variant	rs9379692
Chromosome Location	chr6:24809771-24809772
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	chr6:24720760..24722445-chr6:24809512..24811592,2	K562	blood:
2	chr6:24798986..24801269-chr6:24807888..24810303,2	K562	blood:

Variant related genes	Relation type
ENSG00000260286	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10806993	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10806994	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946728	0.86[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10946729	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946730	0.93[CEU][hapmap];0.88[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]
rs4282395	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4391258	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4397218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4504470	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509111	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513786	0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs4712856	0.81[AMR][1000 genomes]
rs6456636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912790	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6931983	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6931984	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6932132	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6932829	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6932875	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6933295	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7751848	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358804	0.81[AMR][1000 genomes]
rs9379691	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393587	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs9467322	0.82[EUR][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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv5227	chr6:24774149-24824012	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv508396	chr6:24779648-24846309	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9379692	C6orf62	cis	cerebellum	SCAN
rs9379692	HIST1H2BC	cis	cerebellum	SCAN
rs9379692	HIST1H2BI	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24777000-24811600	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:24777000-24847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
4	chr6:24788000-24810200	Weak transcription	Left Ventricle	heart
5	chr6:24788000-24832000	Weak transcription	Brain Substantia Nigra	brain
6	chr6:24788800-24848200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:24789200-24842600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:24798200-24827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:24798200-24841200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:24800000-24843200	Weak transcription	Liver	Liver
11	chr6:24800400-24821800	Weak transcription	Fetal Heart	heart
12	chr6:24800800-24811800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:24800800-24811800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:24801000-24812000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr6:24801200-24811800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr6:24801200-24812000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr6:24801400-24811800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:24801600-24811200	Strong transcription	Primary T cells from cord blood	blood
19	chr6:24802000-24810600	Strong transcription	Primary B cells from cord blood	blood
20	chr6:24802000-24811000	Strong transcription	Primary hematopoietic stem cells	blood
21	chr6:24802000-24811000	Strong transcription	Fetal Thymus	thymus
22	chr6:24802000-24811600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr6:24802000-24811800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:24802000-24811800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:24802000-24812000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:24802400-24811600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:24802400-24811600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:24802400-24811800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:24802400-24811800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:24802600-24810600	Strong transcription	Thymus	Thymus
31	chr6:24802600-24812000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:24802600-24834200	Weak transcription	HSMM	muscle
33	chr6:24802800-24827400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:24803200-24811000	Strong transcription	HSMMtube	muscle
35	chr6:24803400-24810200	Weak transcription	Lung	lung
36	chr6:24803400-24817800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:24803400-24827400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:24804200-24810000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:24804800-24810000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:24804800-24811200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:24804800-24858200	Weak transcription	Gastric	stomach
42	chr6:24805000-24811400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:24805000-24811400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:24805000-24812000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:24805200-24810000	Weak transcription	Right Ventricle	heart
46	chr6:24805800-24810400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:24806200-24810600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:24806200-24810800	Strong transcription	Spleen	Spleen
49	chr6:24806200-24842400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:24806400-24810400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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