Variant report

Variant	rs13389847
Chromosome Location	chr2:85939478-85939479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85932175..85937503-chr2:85937871..85941981,7	K562	blood:
2	chr2:85939136..85942030-chr2:85944013..85946207,3	K562	blood:
3	chr2:85938431..85940449-chr2:85945022..85946831,2	MCF-7	breast:
4	chr2:85939322..85942030-chr2:85943448..85946013,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10180391	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10180445	0.82[CEU][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10180451	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10180547	0.80[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10187164	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10187314	0.81[ASN][1000 genomes]
rs10187495	0.91[ASN][1000 genomes]
rs10192752	0.80[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10203826	0.80[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10206121	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10210321	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11127	0.82[CEU][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12620113	0.97[ASN][1000 genomes]
rs12714150	0.81[ASN][1000 genomes]
rs12845	0.80[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13408224	0.90[ASN][1000 genomes]
rs1437742	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1437743	0.82[CEU][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1437744	0.80[CEU][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1437745	0.80[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1561284	0.80[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1561285	0.80[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1837115	0.80[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1866138	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1866139	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1866140	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1866141	0.80[CEU][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2070966	0.80[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2118402	0.92[ASN][1000 genomes]
rs2366807	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2886767	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2886768	0.90[ASN][1000 genomes]
rs34218330	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34702373	0.96[ASN][1000 genomes]
rs34771575	0.88[ASN][1000 genomes]
rs34943381	0.82[ASN][1000 genomes]
rs3755007	0.87[ASN][1000 genomes]
rs4240200	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4240201	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4240202	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4832181	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4832183	0.81[JPT][hapmap]
rs4832185	0.91[ASN][1000 genomes]
rs4832187	0.82[ASN][1000 genomes]
rs55665393	0.83[ASN][1000 genomes]
rs59832218	0.84[ASN][1000 genomes]
rs61191323	0.91[ASN][1000 genomes]
rs62163092	0.85[ASN][1000 genomes]
rs6740635	0.97[ASN][1000 genomes]
rs7585576	0.97[ASN][1000 genomes]
rs7908	0.80[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs880872	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv874467	chr2:85916487-85946708	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3489943	chr2:85939072-85939531	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3489942	chr2:85939082-85939499	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2030767	chr2:85939088-85939509	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3458037	chr2:85939106-85939491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3270	chr2:85939145-85939535	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13389847	ATOH8	cis	Whole Blood	GTEx
rs13389847	AC012454.4	cis	Whole Blood	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85926000-85945200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:85931200-85941600	Enhancers	Liver	Liver
3	chr2:85931600-85941000	Enhancers	Primary hematopoietic stem cells	blood
4	chr2:85932400-85941400	Enhancers	Brain Hippocampus Middle	brain
5	chr2:85932800-85946600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:85933000-85940200	Weak transcription	Esophagus	oesophagus
7	chr2:85934200-85941400	Enhancers	Brain Anterior Caudate	brain
8	chr2:85934400-85940000	Weak transcription	Pancreas	Pancrea
9	chr2:85934800-85940400	Weak transcription	HMEC	breast
10	chr2:85935800-85941200	Enhancers	Brain Substantia Nigra	brain
11	chr2:85935800-85941400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:85935800-85941400	Enhancers	Ovary	ovary
13	chr2:85936000-85940600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr2:85936200-85940200	Enhancers	Primary B cells from cord blood	blood
15	chr2:85936400-85940600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr2:85936400-85941600	Enhancers	Right Atrium	heart
17	chr2:85936600-85940400	Enhancers	K562	blood
18	chr2:85936600-85940800	Enhancers	Placenta	Placenta
19	chr2:85936600-85941400	Enhancers	Fetal Lung	lung
20	chr2:85937000-85939800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr2:85937000-85940600	Enhancers	Duodenum Mucosa	Duodenum
22	chr2:85937000-85940600	Enhancers	Fetal Thymus	thymus
23	chr2:85937000-85941400	Enhancers	Lung	lung
24	chr2:85937000-85941400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:85937000-85941400	Enhancers	Spleen	Spleen
26	chr2:85937200-85940200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:85937200-85942200	Enhancers	Stomach Mucosa	stomach
28	chr2:85937400-85939600	Weak transcription	Psoas Muscle	Psoas
29	chr2:85937600-85943400	Weak transcription	Fetal Heart	heart
30	chr2:85937800-85941200	Enhancers	Fetal Muscle Leg	muscle
31	chr2:85937800-85944800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:85938000-85940000	Weak transcription	Right Ventricle	heart
33	chr2:85938000-85940200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:85938400-85940200	Weak transcription	Colonic Mucosa	Colon
35	chr2:85938400-85940200	Weak transcription	HSMMtube	muscle
36	chr2:85938400-85941600	Enhancers	Left Ventricle	heart
37	chr2:85938600-85939600	Enhancers	Brain Angular Gyrus	brain
38	chr2:85938600-85940800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:85938600-85941000	Weak transcription	Gastric	stomach
40	chr2:85938800-85939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:85938800-85940000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr2:85938800-85940200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr2:85938800-85941600	Enhancers	Adipose Nuclei	Adipose
44	chr2:85939000-85939600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:85939000-85940000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:85939000-85940000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:85939000-85940000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:85939000-85940000	Weak transcription	Osteobl	bone
49	chr2:85939000-85940200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:85939000-85940200	Weak transcription	Brain Cingulate Gyrus	brain

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