Variant report

Variant	rs13012309
Chromosome Location	chr2:85907924-85907925
allele	A/G
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	SMARCC1	chr2:85907829-85909054	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85895587..85899828-chr2:85904456..85908043,4	K562	blood:
2	chr2:85905086..85909626-chr2:85912458..85918293,6	K562	blood:

Variant related genes	Relation type
GNLY	TF binding region
ENSG00000168878	Chromatin interaction
ENSG00000203363	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10169536	0.80[EUR][1000 genomes]
rs1030862	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12714149	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13011848	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436968	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2366805	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4616480	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4832181	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6547631	0.85[ASN][1000 genomes]
rs934773	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs934774	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874465	chr2:85898898-85939207	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv2812	chr2:85899944-85929267	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13012309	ATOH8	cis	Whole Blood	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85901800-85908800	Weak transcription	HSMMtube	muscle
2	chr2:85903400-85909800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:85905600-85908400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:85905600-85908600	Enhancers	Brain Hippocampus Middle	brain
5	chr2:85905600-85909200	Enhancers	Lung	lung
6	chr2:85905600-85909800	Enhancers	Psoas Muscle	Psoas
7	chr2:85905800-85909600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr2:85906000-85908600	Enhancers	Brain Angular Gyrus	brain
9	chr2:85906200-85909400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:85906400-85908000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:85906400-85908000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:85906400-85908000	Weak transcription	HSMM	muscle
13	chr2:85906400-85908000	Weak transcription	NHDF-Ad	bronchial
14	chr2:85906400-85908600	Weak transcription	NHLF	lung
15	chr2:85906400-85908800	Enhancers	Brain Substantia Nigra	brain
16	chr2:85906400-85914000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:85906600-85908000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:85906600-85908800	Weak transcription	Spleen	Spleen
19	chr2:85906800-85908000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:85906800-85908000	Weak transcription	NH-A	brain
21	chr2:85906800-85909800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr2:85906800-85911400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:85906800-85914400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:85906800-85918400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:85907400-85908800	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:85907400-85909200	Enhancers	Adipose Nuclei	Adipose
27	chr2:85907400-85909200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:85907400-85909400	Enhancers	Left Ventricle	heart
29	chr2:85907400-85909600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:85907400-85909600	Enhancers	Osteobl	bone
31	chr2:85907600-85908000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr2:85907600-85908200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr2:85907600-85908200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr2:85907600-85908200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:85907600-85908200	Enhancers	Brain Anterior Caudate	brain
36	chr2:85907600-85908600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:85907600-85908800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:85907600-85909000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:85907600-85909200	Enhancers	A549	lung
40	chr2:85907800-85908000	Enhancers	Fetal Muscle Leg	muscle
41	chr2:85907800-85908000	Enhancers	Right Atrium	heart
42	chr2:85907800-85909000	Enhancers	Right Ventricle	heart
43	chr2:85907800-85909000	Flanking Active TSS	Hela-S3	cervix
44	chr2:85907800-85909000	Enhancers	HMEC	breast
45	chr2:85907800-85909000	Enhancers	HUVEC	blood vessel

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