Variant report

Variant	rs6680297
Chromosome Location	chr1:221956575-221956576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10495178	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118858	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12022218	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12026940	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12030246	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12034339	0.85[EUR][1000 genomes]
rs12036282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038356	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12039269	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12041329	0.85[EUR][1000 genomes]
rs17010785	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3003901	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58234964	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58787358	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6680316	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680505	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680586	0.97[ASN][1000 genomes]
rs72629678	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9441946	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6680297	hmm26268	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221948800-221958200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:221949400-221958000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:221949800-221958200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr1:221950000-221956800	Enhancers	Fetal Thymus	thymus
5	chr1:221951800-221958000	Enhancers	Primary B cells from cord blood	blood
6	chr1:221952000-221958000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:221953200-221956600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:221953200-221958000	Enhancers	GM12878-XiMat	blood
9	chr1:221953600-221956600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:221954000-221966400	Weak transcription	Spleen	Spleen
11	chr1:221954600-221956800	Enhancers	Thymus	Thymus
12	chr1:221955200-221956800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:221955200-221958000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:221955400-221956600	Enhancers	Primary T cells from cord blood	blood
15	chr1:221955400-221956800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:221955400-221958000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr1:221955600-221956800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:221955600-221958200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:221955600-221958400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:221955800-221956800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:221955800-221958000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:221955800-221958200	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:221956000-221956600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:221956000-221956800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:221956000-221956800	Enhancers	Brain Hippocampus Middle	brain
26	chr1:221956000-221958200	Enhancers	Primary B cells from peripheral blood	blood
27	chr1:221956000-221958200	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:221956000-221958200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:221956200-221956600	Enhancers	H9 Cell Line	embryonic stem cell
30	chr1:221956200-221957000	Enhancers	Brain Anterior Caudate	brain
31	chr1:221956200-221958000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:221956200-221958200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:221956200-221958600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr1:221956200-221960000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:221956400-221957200	Weak transcription	Adipose Nuclei	Adipose
36	chr1:221956400-221957400	Weak transcription	Brain Substantia Nigra	brain
37	chr1:221956400-221958000	Flanking Active TSS	Dnd41	blood

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