Variant report

Variant	rs302992
Chromosome Location	chr6:25062826-25062827
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	chr6:25060649..25063407-chr6:25066068..25067636,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMAHP-1	chr6:25062701-25062888	XLOC_005643
2	lnc-CMAHP-1	chr6:25062701-25062888	XLOC_005643

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1037168	0.81[CEU][hapmap]
rs12524842	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12525328	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12525405	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12528227	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12661796	0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12663160	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12665174	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13195161	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13196712	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13203073	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209444	0.91[EUR][1000 genomes]
rs13218879	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562422	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562423	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1597010	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1597011	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1597012	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs160034	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900551	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923192	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923193	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs192773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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]
rs2273671	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs303879	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];0.95[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]
rs303880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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]
rs303884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34322558	0.92[EUR][1000 genomes]
rs34475409	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34693126	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35028017	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35553146	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36030790	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36078207	0.91[EUR][1000 genomes]
rs3792974	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs3792983	1.00[CEU][hapmap];0.80[CHD][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs3812109	0.85[CEU][hapmap]
rs4711071	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4711072	0.86[ASN][1000 genomes]
rs4711073	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4711075	0.91[EUR][1000 genomes]
rs4712882	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs56108659	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67240854	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67795839	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67927735	0.92[EUR][1000 genomes]
rs72826363	0.84[EUR][1000 genomes]
rs7738141	1.00[CEU][hapmap];0.80[CHD][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs895676	0.96[EUR][1000 genomes];0.88[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	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
2	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
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs302992	HIST1H2BI	cis	cerebellum	SCAN
rs302992	HIST1H1E	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25055400-25064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:25057600-25080400	Weak transcription	Thymus	Thymus
3	chr6:25060400-25063000	Enhancers	Adipose Nuclei	Adipose
4	chr6:25061200-25063200	Enhancers	NHDF-Ad	bronchial
5	chr6:25061200-25065200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:25061400-25063000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:25061400-25063000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr6:25061400-25063000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:25061400-25063000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:25061400-25063200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:25061400-25063200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:25061400-25063200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:25061400-25063200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:25061400-25063200	Enhancers	Fetal Muscle Leg	muscle
15	chr6:25061400-25063400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:25061400-25063600	Enhancers	Fetal Heart	heart
17	chr6:25061400-25065000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:25061600-25063000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:25061600-25063000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:25061600-25063000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:25061600-25063200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr6:25061600-25063200	Enhancers	Ovary	ovary
23	chr6:25061800-25063000	Weak transcription	Left Ventricle	heart
24	chr6:25061800-25063200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:25061800-25063200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:25061800-25066000	Weak transcription	HSMMtube	muscle
27	chr6:25062000-25063000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:25062200-25063000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:25062200-25063000	Enhancers	Osteobl	bone
30	chr6:25062200-25063800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:25062400-25063000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:25062400-25063400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr6:25062800-25063000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:25062800-25063000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:25062800-25063000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:25062800-25063000	Enhancers	Esophagus	oesophagus
37	chr6:25062800-25063200	Enhancers	Fetal Muscle Trunk	muscle
38	chr6:25062800-25063200	Enhancers	Placenta	Placenta
39	chr6:25062800-25064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:25062800-25064200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:25062800-25064200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:25062800-25064200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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