Variant report

Variant	rs61812593
Chromosome Location	chr1:154410490-154410491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154410246..154412652-chr1:154413063..154415706,3	MCF-7	breast:
2	chr1:154409978..154411653-chr1:154414842..154417347,2	MCF-7	breast:
3	chr1:154375871..154378706-chr1:154409907..154412742,3	MCF-7	breast:
4	chr1:154406895..154408731-chr1:154409593..154412430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10159236	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11265618	0.85[ASN][1000 genomes]
rs11804305	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12023358	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12047973	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12048091	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12048950	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4308966	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4329505	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4345796	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845626	0.87[ASN][1000 genomes]
rs55800510	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55826755	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57502626	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812594	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812596	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812599	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61812626	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7529670	0.81[AFR][1000 genomes]
rs7537306	0.85[AFR][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

No data

Chromatin state (count:89 , 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	chr1:154400800-154410600	Strong transcription	Primary T cells from cord blood	blood
3	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:154403800-154417600	Weak transcription	Small Intestine	intestine
5	chr1:154404200-154411400	Weak transcription	Fetal Kidney	kidney
6	chr1:154404400-154411400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:154404600-154412200	Weak transcription	A549	lung
8	chr1:154405400-154410600	Weak transcription	GM12878-XiMat	blood
9	chr1:154405400-154411600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:154405600-154411600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:154405600-154412200	Weak transcription	Psoas Muscle	Psoas
12	chr1:154405600-154413600	Weak transcription	Thymus	Thymus
13	chr1:154405800-154410600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:154405800-154410600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:154405800-154410800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:154405800-154411400	Weak transcription	HepG2	liver
17	chr1:154406000-154411400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:154406000-154412200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:154406200-154410600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:154406200-154410800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:154406200-154411000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr1:154406200-154412600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:154406200-154417600	Weak transcription	Hela-S3	cervix
25	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
26	chr1:154406400-154410600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:154406400-154414000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:154407200-154410600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:154407200-154410800	Weak transcription	Fetal Thymus	thymus
30	chr1:154407200-154413600	Weak transcription	HMEC	breast
31	chr1:154407200-154414000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:154407400-154414200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:154407400-154414400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:154407400-154414600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:154407400-154416200	Genic enhancers	Liver	Liver
36	chr1:154407400-154417400	Weak transcription	Brain Anterior Caudate	brain
37	chr1:154407600-154413800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:154407600-154414000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:154407600-154414000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:154407600-154414200	Weak transcription	Osteobl	bone
41	chr1:154407600-154417200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:154407600-154418600	Weak transcription	Ovary	ovary
43	chr1:154407800-154410600	Weak transcription	Left Ventricle	heart
44	chr1:154408200-154410800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:154408400-154410800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:154408600-154410800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:154408600-154414400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:154408600-154414800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:154408600-154420600	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain

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