Variant report

Variant	rs7546552
Chromosome Location	chr1:154433905-154433906
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154315444..154317958-chr1:154431892..154433961,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10752641	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908839	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229238	0.95[ASN][1000 genomes]
rs35699331	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072391	0.91[ASN][1000 genomes]
rs4240872	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291493	0.82[AMR][1000 genomes]
rs4341355	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379670	0.86[ASN][1000 genomes]
rs4509570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55668699	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427672	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6687597	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698040	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514452	0.95[ASN][1000 genomes]
rs7537291	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537316	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546068	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546555	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs7546552	TDRD10	cis	lung	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154416200-154435800	Strong transcription	Liver	Liver
3	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
4	chr1:154419200-154435800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:154422600-154434400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:154422600-154437600	Weak transcription	Pancreas	Pancrea
7	chr1:154424800-154436000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:154425000-154437200	Weak transcription	Fetal Stomach	stomach
9	chr1:154426000-154434200	Weak transcription	Placenta	Placenta
10	chr1:154426000-154436200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:154426200-154434400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:154426200-154436000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:154426400-154434800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:154426400-154435600	Weak transcription	Stomach Mucosa	stomach
15	chr1:154426400-154436000	Weak transcription	Esophagus	oesophagus
16	chr1:154426400-154436000	Weak transcription	Fetal Lung	lung
17	chr1:154426400-154438000	Weak transcription	Psoas Muscle	Psoas
18	chr1:154426600-154434800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:154426600-154435400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:154426600-154435800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:154426600-154435800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:154426600-154435800	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:154426600-154440600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:154426800-154434400	Weak transcription	Hela-S3	cervix
25	chr1:154426800-154435200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:154426800-154435800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:154426800-154435800	Weak transcription	Osteobl	bone
28	chr1:154426800-154436000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:154426800-154441200	Weak transcription	Brain Substantia Nigra	brain
30	chr1:154426800-154442200	Weak transcription	HepG2	liver
31	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
32	chr1:154427000-154435400	Weak transcription	HMEC	breast
33	chr1:154427000-154435600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:154427400-154435000	Weak transcription	NHDF-Ad	bronchial
35	chr1:154427600-154436000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:154427800-154434200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:154427800-154435600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:154427800-154435600	Weak transcription	NHEK	skin
39	chr1:154427800-154435800	Weak transcription	NHLF	lung
40	chr1:154427800-154436000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:154427800-154464800	Weak transcription	Ovary	ovary
42	chr1:154428600-154437600	Weak transcription	Gastric	stomach
43	chr1:154429400-154436000	Weak transcription	Right Ventricle	heart
44	chr1:154429800-154446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:154430400-154434200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:154430400-154436000	Weak transcription	Spleen	Spleen
47	chr1:154430400-154438800	Weak transcription	Primary B cells from cord blood	blood
48	chr1:154430600-154434800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:154431000-154435800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:154431000-154437400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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