Variant report

Variant	rs4749165
Chromosome Location	chr10:26875066-26875067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr10:26875040-26875190	GM12865	blood:	n/a	n/a
2	CTCF	chr10:26874960-26875110	SAEC	small airway:	n/a	n/a
3	CTCF	chr10:26874960-26875110	GM12866	blood:	n/a	n/a

Variant related genes	Relation type
LINC00264	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11814809	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16927137	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17669071	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2985464	0.81[AFR][1000 genomes]
rs72788603	0.91[ASN][1000 genomes]
rs74128368	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7897115	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv550229	chr10:26848206-26889823	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3332234	chr10:26853285-26881775	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3400546	chr10:26860715-26947192	Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3436664	chr10:26860755-26969397	Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3409599	chr10:26860997-26947298	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv894976	chr10:26861229-26925722	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3351582	chr10:26861352-26915063	Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3360208	chr10:26861751-26915460	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv3221	chr10:26861964-26915516	Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv550231	chr10:26866420-26908475	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv948251	chr10:26869095-26877981	Weak transcription Strong transcription Enhancers Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1049695	chr10:26870254-26914881	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv947775	chr10:26874023-26876784	Active TSS Strong transcription Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv3413883	chr10:26874259-26936074	Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	esv3444410	chr10:26874279-26936044	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4749165	GAD2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26857600-26880200	Weak transcription	Adipose Nuclei	Adipose
2	chr10:26858400-26879400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:26860800-26881200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr10:26860800-26892600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr10:26861000-26886600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:26861200-26884400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr10:26861200-26884800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:26862400-26882400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr10:26863000-26879200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr10:26863200-26875200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr10:26864600-26875800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:26864600-26880400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr10:26864600-26894800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr10:26864800-26875200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr10:26864800-26881800	Weak transcription	Primary B cells from cord blood	blood
16	chr10:26864800-26882800	Weak transcription	Fetal Thymus	thymus
17	chr10:26865000-26884600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:26867200-26884000	Weak transcription	Right Atrium	heart
19	chr10:26872400-26883000	Weak transcription	Gastric	stomach
20	chr10:26874600-26875600	Strong transcription	Thymus	Thymus
21	chr10:26874800-26875400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:26874800-26875400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr10:26874800-26875600	Strong transcription	Spleen	Spleen
24	chr10:26875000-26876000	Strong transcription	Primary T cells from cord blood	blood

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