Variant report

Variant	rs2407093
Chromosome Location	chr13:49157477-49157478
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11148110	0.87[EUR][1000 genomes]
rs12430215	0.81[CEU][hapmap]
rs12877288	0.81[EUR][1000 genomes]
rs12877954	0.88[EUR][1000 genomes]
rs1359688	0.91[EUR][1000 genomes]
rs1536395	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1536396	0.87[EUR][1000 genomes]
rs1536397	0.88[EUR][1000 genomes]
rs1808060	0.82[EUR][1000 genomes]
rs1887152	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1887154	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1951775	0.89[ASW][hapmap];0.95[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs198563	0.85[CEU][hapmap]
rs198584	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs198590	0.85[CEU][hapmap]
rs198612	0.81[CEU][hapmap]
rs2104532	0.88[EUR][1000 genomes]
rs2406935	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2407095	0.88[EUR][1000 genomes]
rs2897588	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4497565	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4635233	0.88[EUR][1000 genomes]
rs6561466	0.81[ASN][1000 genomes]
rs7139578	0.90[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7325719	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7329065	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7332322	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7333360	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7336379	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8002098	0.88[EUR][1000 genomes]
rs9316381	0.85[CEU][hapmap]
rs9316382	0.84[EUR][1000 genomes]
rs9316388	0.85[CEU][hapmap]
rs9316394	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9316395	0.90[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9316399	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs943278	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs943280	0.91[EUR][1000 genomes]
rs943283	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs943284	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9526475	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs9526479	0.83[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526481	0.88[EUR][1000 genomes]
rs9526483	0.87[EUR][1000 genomes]
rs9535032	0.90[ASW][hapmap];0.95[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs9535035	0.84[EUR][1000 genomes]
rs9535038	0.87[EUR][1000 genomes]
rs9535039	0.82[CHB][hapmap]
rs9535041	0.83[ASN][1000 genomes]
rs9535042	0.87[EUR][1000 genomes]
rs9535043	0.85[EUR][1000 genomes]
rs9535045	0.88[EUR][1000 genomes]
rs9535046	0.88[EUR][1000 genomes]
rs9535049	0.81[EUR][1000 genomes]
rs9535059	0.82[AFR][1000 genomes]
rs9562819	0.85[CEU][hapmap]
rs9562828	0.80[ASN][1000 genomes]
rs9568036	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs9568043	0.83[EUR][1000 genomes]
rs9568047	0.82[EUR][1000 genomes]
rs9568049	0.88[EUR][1000 genomes]
rs9568050	0.88[EUR][1000 genomes]
rs9568051	0.83[ASN][1000 genomes]
rs9568059	0.82[AFR][1000 genomes]
rs9568069	0.82[AFR][1000 genomes]
rs9595937	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9634680	0.88[EUR][1000 genomes]
rs964413	0.82[AFR][1000 genomes]
rs990814	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats 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 lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2407093	ATAD2	trans	parietal	SCAN
rs2407093	LPAR6	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49147600-49160800	Weak transcription	Thymus	Thymus
2	chr13:49148400-49158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr13:49148400-49159000	Weak transcription	Pancreas	Pancrea
4	chr13:49148400-49160600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr13:49148800-49157800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr13:49150600-49159400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr13:49153400-49158200	Weak transcription	Fetal Lung	lung
8	chr13:49154000-49158000	Weak transcription	Fetal Muscle Leg	muscle
9	chr13:49154000-49158800	Weak transcription	Right Atrium	heart
10	chr13:49154000-49159000	Weak transcription	Colonic Mucosa	Colon
11	chr13:49154000-49159000	Weak transcription	Esophagus	oesophagus
12	chr13:49154000-49159000	Weak transcription	Left Ventricle	heart
13	chr13:49154000-49159000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:49154000-49159000	Weak transcription	Spleen	Spleen
15	chr13:49154000-49159200	Weak transcription	Placenta	Placenta
16	chr13:49154200-49158000	Weak transcription	Adipose Nuclei	Adipose
17	chr13:49154200-49158600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr13:49154200-49159000	Weak transcription	NHEK	skin
19	chr13:49154200-49159400	Weak transcription	Fetal Thymus	thymus
20	chr13:49154200-49160800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr13:49154200-49160800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:49154400-49158800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr13:49154400-49160200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr13:49154600-49159400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:49154800-49157800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:49154800-49158400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr13:49154800-49158800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:49154800-49158800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr13:49154800-49159000	Weak transcription	Small Intestine	intestine
30	chr13:49154800-49159400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr13:49154800-49159600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:49154800-49160400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr13:49154800-49160400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr13:49154800-49160800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr13:49155000-49158000	Weak transcription	Colon Smooth Muscle	Colon
36	chr13:49155000-49158200	Weak transcription	Brain Substantia Nigra	brain
37	chr13:49155000-49158600	Weak transcription	Brain Anterior Caudate	brain
38	chr13:49155000-49158600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr13:49155000-49158600	Weak transcription	Stomach Mucosa	stomach
40	chr13:49155000-49158800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr13:49155000-49159600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr13:49155000-49160200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr13:49155200-49158200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr13:49155200-49158600	Weak transcription	Brain Hippocampus Middle	brain
45	chr13:49156000-49161400	Enhancers	HepG2	liver
46	chr13:49156400-49158800	Weak transcription	Right Ventricle	heart
47	chr13:49156400-49161400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:49156600-49157800	Weak transcription	Fetal Intestine Small	intestine
49	chr13:49157200-49158400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr13:49157400-49157600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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