Variant report

Variant	rs13192978
Chromosome Location	chr6:24885300-24885301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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]
rs13211772	1.00[CEU][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]
rs13215106	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207401	1.00[ASN][1000 genomes]
rs2747678	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747679	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]
rs35158242	1.00[ASN][1000 genomes]
rs35250553	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35953835	1.00[ASN][1000 genomes]
rs61595405	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456637	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914915	0.81[AFR][1000 genomes];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
rs13192978	HIST1H4H	cis	cerebellum	SCAN
rs13192978	HIST1H2BD	cis	parietal	SCAN
rs13192978	HIST1H3A	cis	cerebellum	SCAN
rs13192978	HIST1H2AC	cis	parietal	SCAN
rs13192978	HIST1H2BC	cis	cerebellum	SCAN
rs13192978	HIST1H2BB	cis	cerebellum	SCAN

Chromatin state (count:57 , 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	chr6:24859400-24886800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:24862800-24885600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:24862800-24887400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
5	chr6:24871800-24886800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:24875600-24886800	Weak transcription	Fetal Heart	heart
7	chr6:24875800-24887800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
9	chr6:24877000-24888000	Genic enhancers	Primary T cells from cord blood	blood
10	chr6:24877400-24888000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:24878400-24887800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr6:24878400-24899800	Weak transcription	Thymus	Thymus
13	chr6:24878800-24885400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr6:24879200-24888200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:24880000-24889200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:24880200-24886600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:24880400-24888000	Weak transcription	Brain Germinal Matrix	brain
18	chr6:24880600-24886400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:24880600-24886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:24880600-24886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:24880600-24887200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:24881000-24886400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:24881200-24898400	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr6:24881400-24895400	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr6:24881600-24888400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:24881800-24891000	Weak transcription	Psoas Muscle	Psoas
27	chr6:24882000-24885600	Genic enhancers	Primary B cells from cord blood	blood
28	chr6:24882000-24887000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:24882400-24886800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:24882400-24904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:24882600-24899200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:24883200-24886400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:24883800-24885800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:24883800-24886800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:24883800-24887400	Weak transcription	HSMMtube	muscle
36	chr6:24883800-24887800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:24883800-24888200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr6:24884000-24885600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:24884000-24886000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:24884000-24889600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:24884200-24886800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:24884200-24887400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:24884200-24888000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:24884200-24888000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:24884200-24888000	Weak transcription	Brain Anterior Caudate	brain
47	chr6:24884200-24888200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:24884200-24891000	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:24884200-24899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:24884400-24887600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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