Variant report

Variant	rs17533873
Chromosome Location	chr1:222958670-222958671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222928279..222930727-chr1:222957957..222960468,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11490203	0.83[EUR][1000 genomes]
rs11490204	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11490205	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163484	0.95[ASN][1000 genomes]
rs17474556	0.82[ASN][1000 genomes]
rs17474745	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17533651	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17533810	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378602	0.94[ASN][1000 genomes]
rs2889937	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2889940	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34251271	0.95[ASN][1000 genomes]
rs34311160	0.83[EUR][1000 genomes]
rs34430931	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34494528	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34643154	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34687048	0.94[ASN][1000 genomes]
rs34807177	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35292789	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35325797	0.94[ASN][1000 genomes]
rs35472374	0.94[ASN][1000 genomes]
rs35554894	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35651802	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35840203	0.94[ASN][1000 genomes]
rs35976854	0.97[ASN][1000 genomes]
rs3922772	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4011743	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240935	0.84[EUR][1000 genomes]
rs4264001	0.95[ASN][1000 genomes]
rs4303078	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4322239	0.94[ASN][1000 genomes]
rs4424514	0.95[ASN][1000 genomes]
rs4472762	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4480364	0.94[ASN][1000 genomes]
rs4562632	0.97[ASN][1000 genomes]
rs4846387	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61826464	0.94[ASN][1000 genomes]
rs61826465	0.94[ASN][1000 genomes]
rs61826467	0.94[ASN][1000 genomes]
rs61826474	0.95[ASN][1000 genomes]
rs61837141	0.95[ASN][1000 genomes]
rs61837143	0.95[ASN][1000 genomes]
rs61837144	0.88[ASN][1000 genomes]
rs61837147	0.95[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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222947200-222959200	Weak transcription	Fetal Brain Male	brain
2	chr1:222948200-222961600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:222951400-222959400	Weak transcription	Stomach Mucosa	stomach
4	chr1:222951600-222959600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:222953400-222968000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:222956400-222960000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:222957000-222959000	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:222957200-222960400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:222957200-222960400	Enhancers	Hela-S3	cervix
10	chr1:222957400-222961600	Enhancers	Fetal Lung	lung
11	chr1:222957600-222959000	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:222957600-222959000	Weak transcription	Placenta	Placenta
13	chr1:222957800-222960200	Enhancers	HUVEC	blood vessel
14	chr1:222958000-222959000	Enhancers	Brain Substantia Nigra	brain
15	chr1:222958000-222959400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:222958200-222958800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:222958200-222959200	Enhancers	Fetal Kidney	kidney
18	chr1:222958200-222959400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:222958200-222959400	Weak transcription	Brain Anterior Caudate	brain
20	chr1:222958400-222958800	Enhancers	Rectal Smooth Muscle	rectum
21	chr1:222958400-222959000	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:222958400-222959200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:222958400-222959400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:222958600-222959600	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:222958600-222959600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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