Variant report

Variant	rs2747682
Chromosome Location	chr6:24884149-24884150
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2255339	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2474149	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2493330	0.85[ASN][1000 genomes]
rs2747680	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2747681	0.87[ASN][1000 genomes]
rs2817714	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2817721	0.85[ASN][1000 genomes]
rs2817725	0.89[YRI][hapmap]
rs2817751	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9356948	0.85[ASN][1000 genomes]
rs9358807	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2747682	HIST1H2BC	cis	cerebellum	SCAN
rs2747682	HIST1H2BJ	cis	parietal	SCAN

Chromatin state (count:68 , 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	chr6:24879800-24884400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:24880000-24889200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:24880200-24886600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:24880400-24888000	Weak transcription	Brain Germinal Matrix	brain
19	chr6:24880600-24886400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:24880600-24886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:24880600-24886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:24880600-24887200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:24881000-24886400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:24881200-24898400	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr6:24881400-24895400	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr6:24881600-24888400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:24881800-24891000	Weak transcription	Psoas Muscle	Psoas
28	chr6:24882000-24884200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:24882000-24884400	Enhancers	NHDF-Ad	bronchial
30	chr6:24882000-24885600	Genic enhancers	Primary B cells from cord blood	blood
31	chr6:24882000-24887000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:24882400-24884200	Enhancers	NHLF	lung
33	chr6:24882400-24886800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:24882400-24904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:24882600-24884200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr6:24882600-24884400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:24882600-24899200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:24883200-24884200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:24883200-24884200	Enhancers	Brain Anterior Caudate	brain
40	chr6:24883200-24884200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:24883200-24884200	Enhancers	HSMM	muscle
42	chr6:24883200-24884400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:24883200-24886400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:24883400-24884200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr6:24883400-24884200	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr6:24883400-24884200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:24883400-24884200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:24883400-24884200	Enhancers	Fetal Muscle Leg	muscle
49	chr6:24883400-24884400	Flanking Active TSS	GM12878-XiMat	blood
50	chr6:24883400-24885000	Enhancers	Dnd41	blood

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