Variant report

Variant	rs2747679
Chromosome Location	chr6:24888842-24888843
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	chr6:24886932..24889489-chr6:24891782..24893899,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10946732	1.00[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs10946735	0.89[GIH][hapmap];0.88[MEX][hapmap]
rs12110779	0.81[EUR][1000 genomes]
rs12111413	1.00[ASN][1000 genomes]
rs13192978	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211772	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215106	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220782	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889761	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17671350	0.94[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs2207400	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207401	1.00[ASN][1000 genomes]
rs2747678	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35158242	1.00[ASN][1000 genomes]
rs35250553	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35953835	1.00[ASN][1000 genomes]
rs61595405	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456637	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914915	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918387	1.00[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs6918511	1.00[ASN][1000 genomes]
rs71555168	1.00[ASN][1000 genomes]
rs7760221	0.80[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2747679	HIST1H2AC	cis	parietal	SCAN
rs2747679	HIST1H2BC	cis	cerebellum	SCAN
rs2747679	HIST1H2BB	cis	cerebellum	SCAN
rs2747679	HIST1H3A	cis	cerebellum	SCAN
rs2747679	HIST1H2BD	cis	parietal	SCAN
rs2747679	HIST1H4H	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	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
3	chr6:24878400-24899800	Weak transcription	Thymus	Thymus
4	chr6:24880000-24889200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:24881200-24898400	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr6:24881400-24895400	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr6:24881800-24891000	Weak transcription	Psoas Muscle	Psoas
8	chr6:24882400-24904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:24882600-24899200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:24884000-24889600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:24884200-24891000	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:24884200-24899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:24885600-24891200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr6:24885600-24896600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:24885800-24890000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr6:24886400-24889400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr6:24886600-24895000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:24886800-24889400	Enhancers	Fetal Heart	heart
20	chr6:24886800-24889600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:24887000-24889600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:24887000-24890200	Genic enhancers	Primary B cells from cord blood	blood
23	chr6:24887000-24894000	Weak transcription	Fetal Thymus	thymus
24	chr6:24887000-24900000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:24887200-24889200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:24887200-24889400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr6:24887200-24889600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:24887400-24889600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:24887400-24889600	Enhancers	HSMMtube	muscle
30	chr6:24887400-24889800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:24887400-24897400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:24887400-24898000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:24887600-24889600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:24887800-24889000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:24887800-24889400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:24887800-24889400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:24887800-24890800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:24887800-24891000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr6:24888000-24889400	Enhancers	Brain Anterior Caudate	brain
40	chr6:24888000-24889800	Enhancers	Brain Germinal Matrix	brain
41	chr6:24888200-24889000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:24888200-24889400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr6:24888200-24890000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:24888200-24892600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr6:24888200-24897400	Weak transcription	Fetal Brain Female	brain
46	chr6:24888400-24889000	Enhancers	GM12878-XiMat	blood
47	chr6:24888400-24889200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:24888400-24889800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:24888400-24891400	Weak transcription	NHDF-Ad	bronchial
50	chr6:24888600-24889000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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