Variant report

Variant	rs2747680
Chromosome Location	chr6:24887485-24887486
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	chr6:24886932..24889489-chr6:24891782..24893899,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2255339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2474149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[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]
rs2493330	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2747681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747682	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2817714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817721	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817722	1.00[YRI][hapmap]
rs2817730	0.82[EUR][1000 genomes]
rs2817750	0.88[EUR][1000 genomes]
rs2817751	0.84[ASN][1000 genomes]
rs4712861	0.80[CEU][hapmap]
rs9356948	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9358807	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2747680	HIST1H3H	cis	cerebellum	SCAN
rs2747680	EIF3J	trans	parietal	SCAN
rs2747680	ZNF204P	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24855200-24895000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
2	chr6:24875800-24887800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
4	chr6:24877000-24888000	Genic enhancers	Primary T cells from cord blood	blood
5	chr6:24877400-24888000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:24878400-24887800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr6:24878400-24899800	Weak transcription	Thymus	Thymus
8	chr6:24879200-24888200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr6:24880000-24889200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:24880400-24888000	Weak transcription	Brain Germinal Matrix	brain
11	chr6:24881200-24898400	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr6:24881400-24895400	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr6:24881600-24888400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:24881800-24891000	Weak transcription	Psoas Muscle	Psoas
15	chr6:24882400-24904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:24882600-24899200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:24883800-24887800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:24883800-24888200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:24884000-24889600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:24884200-24888000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:24884200-24888000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:24884200-24888000	Weak transcription	Brain Anterior Caudate	brain
24	chr6:24884200-24888200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:24884200-24891000	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:24884200-24899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:24884400-24887600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:24885000-24887600	Weak transcription	NHDF-Ad	bronchial
29	chr6:24885600-24891200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr6:24885600-24896600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:24885800-24890000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr6:24886400-24888000	Enhancers	GM12878-XiMat	blood
33	chr6:24886400-24889400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr6:24886600-24888200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:24886600-24888600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr6:24886600-24895000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr6:24886800-24887800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:24886800-24888400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:24886800-24888800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr6:24886800-24889400	Enhancers	Fetal Heart	heart
41	chr6:24886800-24889600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr6:24887000-24889600	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr6:24887000-24890200	Genic enhancers	Primary B cells from cord blood	blood
44	chr6:24887000-24894000	Weak transcription	Fetal Thymus	thymus
45	chr6:24887000-24900000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:24887200-24889200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:24887200-24889400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:24887200-24889600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:24887400-24887800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:24887400-24888200	Enhancers	Primary T helper cells PMA-I stimulated	--

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