Variant report

Variant	rs13060869
Chromosome Location	chr3:134369716-134369717
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11720224	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13071253	1.00[JPT][hapmap]
rs13071852	1.00[JPT][hapmap]
rs13079012	1.00[JPT][hapmap]
rs13081172	0.94[ASN][1000 genomes]
rs13083717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13085889	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs13098689	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34136671	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34701532	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57936237	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60716777	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762606	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637801	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][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	nsv877510	chr3:134126150-134400448	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv877512	chr3:134174071-134372486	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv877513	chr3:134174071-134379752	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv877514	chr3:134191938-134372486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv3343656	chr3:134368312-134371210	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13060869	TXNDC6	cis	cerebellum	SCAN
rs13060869	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs13060869	ANAPC13	cis	Nerve Tibial	GTEx
rs13060869	KY	cis	cerebellum	SCAN
rs13060869	ANAPC13	cis	Esophagus Mucosa	GTEx
rs13060869	CEP63	cis	multi-tissue	Pritchard
rs13060869	ANAPC13	cis	cerebellum	SCAN
rs13060869	ANAPC13	cis	parietal	SCAN
rs13060869	ANAPC13	cis	Esophagus Muscularis	GTEx
rs13060869	ANAPC13	cis	Muscle Skeletal	GTEx
rs13060869	ANAPC13	cis	Artery Tibial	GTEx
rs13060869	ANAPC13	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134367000-134369800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:134368200-134371200	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr3:134368400-134371800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:134368600-134370200	Active TSS	Rectal Smooth Muscle	rectum
5	chr3:134368800-134370200	Active TSS	Brain Angular Gyrus	brain
6	chr3:134368800-134370200	Active TSS	Brain Hippocampus Middle	brain
7	chr3:134368800-134370200	Active TSS	Brain Substantia Nigra	brain
8	chr3:134369000-134370000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:134369000-134370400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:134369000-134370600	Active TSS	Colon Smooth Muscle	Colon
11	chr3:134369000-134370600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr3:134369000-134370800	Active TSS	Brain Anterior Caudate	brain
13	chr3:134369200-134370000	Active TSS	Muscle Satellite Cultured Cells	--
14	chr3:134369200-134370000	Active TSS	Left Ventricle	heart
15	chr3:134369200-134370200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:134369200-134370200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr3:134369200-134370200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr3:134369200-134370200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr3:134369200-134370200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:134369200-134370200	Active TSS	Brain Cingulate Gyrus	brain
21	chr3:134369200-134370200	Active TSS	Duodenum Mucosa	Duodenum
22	chr3:134369200-134370200	Active TSS	Fetal Intestine Small	intestine
23	chr3:134369200-134370200	Active TSS	Psoas Muscle	Psoas
24	chr3:134369200-134370400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr3:134369200-134370400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
26	chr3:134369200-134370400	Enhancers	Spleen	Spleen
27	chr3:134369200-134370600	Bivalent/Poised TSS	Fetal Brain Female	brain
28	chr3:134369200-134370800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:134369200-134370800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:134369200-134370800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr3:134369200-134370800	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:134369200-134371000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:134369200-134371000	Enhancers	Lung	lung
34	chr3:134369400-134369800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr3:134369400-134369800	Active TSS	Primary hematopoietic stem cells	blood
36	chr3:134369400-134369800	Flanking Active TSS	HSMM	muscle
37	chr3:134369400-134370000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr3:134369400-134370000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr3:134369400-134370000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:134369400-134370000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:134369400-134370000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:134369400-134370000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr3:134369400-134370000	Bivalent/Poised TSS	Fetal Stomach	stomach
44	chr3:134369400-134370200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:134369400-134370200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr3:134369400-134370200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:134369400-134370200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr3:134369400-134370200	Enhancers	Liver	Liver
49	chr3:134369400-134370200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:134369400-134370200	Active TSS	Esophagus	oesophagus

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