Variant report

Variant	rs333687
Chromosome Location	chr10:20128272-20128273
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	chr10:20119224..20121813-chr10:20126218..20128870,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10764159	0.86[EUR][1000 genomes]
rs10764164	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10827885	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12257233	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1590963	0.82[ASN][1000 genomes]
rs1977539	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2481936	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481937	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481938	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2481939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2884470	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs333689	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs333691	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333692	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs420898	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs442830	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs447706	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4748612	0.90[ASN][1000 genomes]
rs6482065	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7086438	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7094033	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7906452	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7908480	0.85[ASN][1000 genomes]
rs7911243	0.86[ASN][1000 genomes]
rs7912855	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7914865	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7914996	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs989767	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][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	nsv1049295	chr10:19740296-20509036	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1044794	chr10:20010269-20391329	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv540510	chr10:20010269-20391329	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1038966	chr10:20010469-20391190	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv540511	chr10:20010469-20391190	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1037055	chr10:20010469-20651965	Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv540512	chr10:20010469-20651965	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:20110400-20151400	Weak transcription	Fetal Intestine Small	intestine
2	chr10:20115200-20154000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr10:20118200-20136200	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:20122200-20132600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr10:20122400-20131200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:20122400-20132600	Weak transcription	Psoas Muscle	Psoas
7	chr10:20122400-20133600	Weak transcription	Left Ventricle	heart
8	chr10:20122600-20131400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr10:20122600-20136000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:20122800-20149000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:20124400-20128400	Weak transcription	Esophagus	oesophagus
12	chr10:20126200-20142600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr10:20126400-20132600	Weak transcription	Fetal Stomach	stomach
14	chr10:20126600-20128400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr10:20126600-20131200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr10:20126600-20132400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:20126800-20128400	Weak transcription	Fetal Lung	lung
18	chr10:20126800-20128600	Weak transcription	Fetal Kidney	kidney
19	chr10:20126800-20130000	Weak transcription	Brain Hippocampus Middle	brain
20	chr10:20127000-20130800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr10:20127400-20128600	Enhancers	Brain Cingulate Gyrus	brain
22	chr10:20127800-20128400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr10:20127800-20128400	Enhancers	Aorta	Aorta
24	chr10:20127800-20129200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr10:20128000-20128400	Weak transcription	Brain Angular Gyrus	brain
26	chr10:20128000-20128400	Enhancers	Ovary	ovary
27	chr10:20128000-20128600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:20128000-20128800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr10:20128000-20128800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:20128000-20129000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr10:20128200-20128400	Enhancers	Small Intestine	intestine
32	chr10:20128200-20129000	Enhancers	Brain Anterior Caudate	brain
33	chr10:20128200-20129200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr10:20128200-20129200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr10:20128200-20129200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr10:20128200-20129200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr10:20128200-20130200	Enhancers	Brain Substantia Nigra	brain
38	chr10:20128200-20134000	Weak transcription	Right Atrium	heart

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