Variant report

Variant	rs2489583
Chromosome Location	chr10:26987698-26987699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:26954305..26956450-chr10:26987430..26988975,2	K562	blood:
2	chr10:26985323..26988042-chr10:27148387..27150466,3	MCF-7	breast:
3	chr10:26986021..26987940-chr10:27149008..27151636,2	MCF-7	breast:
4	chr10:26985752..26988058-chr10:26992017..26994907,3	MCF-7	breast:
5	chr10:26986198..26989615-chr10:27022506..27024765,3	MCF-7	breast:
6	chr10:26986774..26988762-chr10:27020723..27023686,2	K562	blood:

Variant related genes	Relation type
ENSG00000136754	Chromatin interaction
ENSG00000148459	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1031859	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1031860	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs1148159	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1148160	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1197422	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1408529	0.95[CEU][hapmap]
rs1564271	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1616702	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1631468	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1677722	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1748332	0.95[CEU][hapmap]
rs1748333	0.81[ASW][hapmap];0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1748335	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1780191	0.81[EUR][1000 genomes]
rs1824851	1.00[ASW][hapmap]
rs1830844	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1853686	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980755	0.92[ASN][1000 genomes]
rs1980756	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2209350	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2252096	0.81[ASW][hapmap];0.95[CEU][hapmap];0.95[JPT][hapmap]
rs2448127	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2477266	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs2477292	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489589	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv1798973	chr10:26968171-27001814	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv550233	chr10:26968171-27011323	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2489583	TPRT	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26985400-26988600	Active TSS	GM12878-XiMat	blood
2	chr10:26985600-26987800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:26985600-26987800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr10:26985600-26988000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr10:26985600-26988200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:26985600-26988200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr10:26985600-26988200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr10:26985600-26988200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr10:26985600-26988200	Active TSS	A549	lung
10	chr10:26985600-26988400	Active TSS	Psoas Muscle	Psoas
11	chr10:26985800-26987800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr10:26985800-26988000	Active TSS	Thymus	Thymus
13	chr10:26986000-26987800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:26986000-26987800	Active TSS	Fetal Intestine Large	intestine
15	chr10:26986000-26987800	Active TSS	HMEC	breast
16	chr10:26986000-26987800	Active TSS	NHDF-Ad	bronchial
17	chr10:26986000-26987800	Active TSS	NHEK	skin
18	chr10:26986000-26988000	Active TSS	HSMM	muscle
19	chr10:26986000-26988200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr10:26986800-26987800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:26986800-26987800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr10:26987000-26987800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr10:26987000-26987800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr10:26987000-26987800	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr10:26987000-26988000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr10:26987000-26988000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr10:26987000-26988200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:26987000-26988200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr10:26987000-26988200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr10:26987000-26989000	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr10:26987200-26987800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:26987200-26987800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr10:26987200-26987800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr10:26987200-26987800	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr10:26987200-26987800	Flanking Active TSS	HUVEC	blood vessel
36	chr10:26987200-26987800	Flanking Active TSS	NH-A	brain
37	chr10:26987200-26987800	Flanking Active TSS	NHLF	lung
38	chr10:26987200-26988000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:26987200-26988000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr10:26987200-26988000	Flanking Active TSS	Dnd41	blood
41	chr10:26987200-26988200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr10:26987200-26988200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr10:26987200-26988200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr10:26987200-26988400	Flanking Active TSS	Fetal Thymus	thymus
45	chr10:26987200-26988400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr10:26987400-26987800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:26987400-26987800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:26987400-26987800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:26987400-26987800	Flanking Active TSS	Fetal Brain Female	brain
50	chr10:26987400-26987800	Flanking Active TSS	Fetal Intestine Small	intestine

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