Variant report

Variant	rs2478143
Chromosome Location	chr10:20121877-20121878
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	chr10:20119404..20122160-chr10:20290865..20292998,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10764158	0.81[ASN][1000 genomes]
rs1116210	0.81[ASN][1000 genomes]
rs12242699	0.89[ASN][1000 genomes]
rs1977538	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2478144	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481935	0.91[ASN][1000 genomes]
rs333688	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs372542	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs391559	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4475831	0.87[ASN][1000 genomes]
rs4748611	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6482066	0.96[ASN][1000 genomes]
rs7076946	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7894992	0.89[ASN][1000 genomes]
rs7908024	0.97[ASN][1000 genomes]
rs7922577	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7924250	0.91[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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:20110400-20151400	Weak transcription	Fetal Intestine Small	intestine
2	chr10:20114000-20125200	Weak transcription	Fetal Kidney	kidney
3	chr10:20115200-20154000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr10:20118000-20123800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:20118000-20124000	Weak transcription	Right Ventricle	heart
6	chr10:20118200-20122200	Weak transcription	HSMMtube	muscle
7	chr10:20118200-20136200	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:20118600-20122000	Weak transcription	Fetal Muscle Leg	muscle
9	chr10:20118600-20126200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:20119000-20122000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:20119600-20123000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:20119800-20127800	Weak transcription	Aorta	Aorta
13	chr10:20121000-20123000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr10:20121200-20122400	Enhancers	Brain Cingulate Gyrus	brain
15	chr10:20121200-20122600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:20121200-20124000	Enhancers	Fetal Lung	lung
17	chr10:20121400-20122200	Flanking Active TSS	HMEC	breast
18	chr10:20121400-20122600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr10:20121400-20122600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr10:20121400-20122800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr10:20121600-20122000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr10:20121600-20122000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:20121600-20122000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr10:20121600-20122000	Enhancers	Ovary	ovary
25	chr10:20121600-20122200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr10:20121600-20122200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:20121600-20122400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:20121600-20122400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr10:20121600-20122400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:20121600-20122400	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr10:20121600-20122400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr10:20121600-20122400	Enhancers	Lung	lung
33	chr10:20121600-20122400	Enhancers	Psoas Muscle	Psoas
34	chr10:20121600-20122400	Enhancers	Right Atrium	heart
35	chr10:20121600-20122400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr10:20121600-20122600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr10:20121600-20122600	Enhancers	H9 Cell Line	embryonic stem cell
38	chr10:20121600-20122600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:20121600-20122600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr10:20121600-20122600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr10:20121600-20122600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:20121600-20122600	Enhancers	Brain Anterior Caudate	brain
43	chr10:20121600-20122600	Enhancers	Brain Substantia Nigra	brain
44	chr10:20121600-20122600	Enhancers	NH-A	brain
45	chr10:20121600-20122600	Flanking Active TSS	NHEK	skin
46	chr10:20121600-20122800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr10:20121600-20123200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:20121600-20123200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr10:20121600-20123600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr10:20121800-20122000	Flanking Active TSS	Brain Angular Gyrus	brain

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