Variant report

Variant	rs2328878
Chromosome Location	chr6:25297685-25297686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCGN-4	chr6:25297378-25298038	NONHSAT108152

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12055533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12196702	0.81[ASN][1000 genomes]
rs1989206	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2143022	0.88[CEU][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252012	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2690109	0.81[ASN][1000 genomes]
rs2690115	0.84[ASN][1000 genomes]
rs2690120	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690123	0.96[ASN][1000 genomes]
rs2690125	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690127	0.94[ASN][1000 genomes]
rs2690129	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690131	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744290	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2744296	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744299	0.84[CEU][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744302	0.82[ASN][1000 genomes]
rs2744303	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4712908	0.87[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9348670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356973	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358850	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358851	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9379751	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MEX][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467465	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][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	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2328878	HIST1H3B	cis	cerebellum	SCAN
rs2328878	HIST1H2BL	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25286800-25300800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:25288600-25301200	Weak transcription	Brain Anterior Caudate	brain
4	chr6:25289000-25298600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:25289000-25300600	Weak transcription	Pancreas	Pancrea
6	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:25292200-25303000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:25292400-25301000	Weak transcription	Adipose Nuclei	Adipose
9	chr6:25293000-25301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:25293200-25301200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:25293800-25298000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:25294200-25311200	Weak transcription	Lung	lung
13	chr6:25294600-25301600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:25295000-25297800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:25295600-25299400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:25295800-25297800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:25295800-25297800	Enhancers	Thymus	Thymus
18	chr6:25295800-25298000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:25295800-25298000	Enhancers	Fetal Intestine Small	intestine
20	chr6:25295800-25298000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr6:25295800-25298000	Enhancers	Small Intestine	intestine
22	chr6:25295800-25298000	Enhancers	NHDF-Ad	bronchial
23	chr6:25295800-25298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:25295800-25298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:25295800-25298200	Enhancers	Fetal Heart	heart
26	chr6:25295800-25298200	Enhancers	HSMMtube	muscle
27	chr6:25295800-25299200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:25296000-25297800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:25296000-25297800	Enhancers	Fetal Thymus	thymus
30	chr6:25296000-25298000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:25296000-25299200	Enhancers	Fetal Lung	lung
32	chr6:25296000-25301200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:25296400-25298000	Enhancers	Ovary	ovary
34	chr6:25296400-25298000	Enhancers	Stomach Mucosa	stomach
35	chr6:25296400-25298200	Enhancers	Primary hematopoietic stem cells	blood
36	chr6:25296400-25302400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:25296600-25298000	Enhancers	Fetal Stomach	stomach
38	chr6:25296600-25298000	Enhancers	Stomach Smooth Muscle	stomach
39	chr6:25296600-25298200	Enhancers	Fetal Kidney	kidney
40	chr6:25296600-25301200	Weak transcription	Brain Substantia Nigra	brain
41	chr6:25296600-25302400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:25296600-25302600	Weak transcription	Colonic Mucosa	Colon
43	chr6:25296800-25301800	Weak transcription	Fetal Intestine Large	intestine
44	chr6:25296800-25302200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:25297000-25298400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:25297000-25298600	Weak transcription	HMEC	breast
47	chr6:25297000-25299000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:25297000-25299000	Weak transcription	Right Atrium	heart
49	chr6:25297000-25300600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:25297000-25300600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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