Variant report

Variant	rs59632925
Chromosome Location	chr1:154406540-154406541
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154401123..154404227-chr1:154404483..154407452,3	MCF-7	breast:
2	chr1:154383846..154386269-chr1:154404015..154406956,2	K562	blood:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10908837	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10908838	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265611	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11265612	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12117832	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12118721	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118770	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12129500	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4553185	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845371	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845372	0.80[AFR][1000 genomes]
rs4845618	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845619	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845625	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6427658	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667434	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6683206	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6686750	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6687726	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689306	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689393	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6694258	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6694817	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526131	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7536152	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7549250	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549338	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553796	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59632925	TDRD10	cis	lung	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154397000-154414200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:154399400-154407200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:154399600-154406800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:154399600-154409200	Enhancers	Placenta	Placenta
5	chr1:154400800-154410600	Strong transcription	Primary T cells from cord blood	blood
6	chr1:154401200-154406600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
7	chr1:154401800-154407000	Enhancers	NHEK	skin
8	chr1:154401800-154407200	Weak transcription	Pancreas	Pancrea
9	chr1:154402000-154406600	Genic enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:154402200-154406800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:154402200-154407600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:154402400-154407200	Enhancers	HMEC	breast
13	chr1:154402400-154407800	Enhancers	Fetal Heart	heart
14	chr1:154402600-154407000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:154402600-154407400	Enhancers	NHDF-Ad	bronchial
16	chr1:154402800-154407200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:154403200-154406800	Weak transcription	Fetal Brain Male	brain
18	chr1:154403200-154408000	Enhancers	Right Ventricle	heart
19	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
20	chr1:154403600-154406800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:154403600-154407000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:154403800-154407000	Weak transcription	Ovary	ovary
23	chr1:154403800-154407000	Enhancers	Stomach Mucosa	stomach
24	chr1:154403800-154417600	Weak transcription	Small Intestine	intestine
25	chr1:154404000-154406800	Enhancers	Colon Smooth Muscle	Colon
26	chr1:154404000-154407200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:154404000-154407200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:154404200-154406800	Enhancers	Esophagus	oesophagus
29	chr1:154404200-154411400	Weak transcription	Fetal Kidney	kidney
30	chr1:154404400-154406800	Enhancers	Adipose Nuclei	Adipose
31	chr1:154404400-154407000	Weak transcription	Gastric	stomach
32	chr1:154404400-154411400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:154404600-154412200	Weak transcription	A549	lung
34	chr1:154404800-154406600	Weak transcription	Osteobl	bone
35	chr1:154404800-154407000	Weak transcription	HSMMtube	muscle
36	chr1:154404800-154407000	Weak transcription	K562	blood
37	chr1:154405200-154406800	Enhancers	Brain Hippocampus Middle	brain
38	chr1:154405200-154407000	Enhancers	Fetal Muscle Leg	muscle
39	chr1:154405200-154407600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:154405400-154407600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:154405400-154410600	Weak transcription	GM12878-XiMat	blood
42	chr1:154405400-154411600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:154405600-154406800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:154405600-154406800	Genic enhancers	Rectal Mucosa Donor 29	rectum
45	chr1:154405600-154407200	Enhancers	Fetal Lung	lung
46	chr1:154405600-154409400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:154405600-154409800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:154405600-154411600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:154405600-154412200	Weak transcription	Psoas Muscle	Psoas
50	chr1:154405600-154413600	Weak transcription	Thymus	Thymus

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