Variant report

Variant	rs10797058
Chromosome Location	chr1:154200704-154200705
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	chr1:154199628..154201203-chr1:154208732..154211600,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10797061	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10908739	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10908751	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11265285	0.87[EUR][1000 genomes]
rs1194580	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1194582	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1194599	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1194600	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1194602	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1194603	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1194604	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12044616	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12063830	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12095767	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2220390	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4072431	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4364874	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4393149	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4579747	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845609	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4845610	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6680947	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7516809	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7526644	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7533952	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9803862	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9804045	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9943097	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	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
5	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
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10797058	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154194600-154201000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:154194600-154201000	Weak transcription	Aorta	Aorta
3	chr1:154194600-154201000	Weak transcription	Esophagus	oesophagus
4	chr1:154194600-154201000	Weak transcription	Pancreas	Pancrea
5	chr1:154194800-154202000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:154195200-154211400	Weak transcription	Right Atrium	heart
7	chr1:154195400-154234600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:154195800-154204000	Weak transcription	Stomach Mucosa	stomach
10	chr1:154196200-154203200	Weak transcription	Fetal Brain Male	brain
11	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:154196400-154218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:154196600-154237600	Strong transcription	Fetal Thymus	thymus
15	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:154196800-154211800	Strong transcription	NHEK	skin
17	chr1:154196800-154224200	Strong transcription	K562	blood
18	chr1:154196800-154224400	Strong transcription	Primary B cells from cord blood	blood
19	chr1:154196800-154235800	Strong transcription	HUVEC	blood vessel
20	chr1:154196800-154242600	Strong transcription	A549	lung
21	chr1:154197000-154235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:154197200-154205000	Strong transcription	NHDF-Ad	bronchial
28	chr1:154197200-154210800	Strong transcription	HMEC	breast
29	chr1:154197200-154214200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:154197400-154203400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:154197400-154212200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:154197400-154224200	Strong transcription	Hela-S3	cervix
35	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
36	chr1:154197600-154201200	Weak transcription	Fetal Heart	heart
37	chr1:154197600-154201800	Strong transcription	Fetal Kidney	kidney
38	chr1:154197600-154202800	Strong transcription	Spleen	Spleen
39	chr1:154197600-154203600	Strong transcription	NH-A	brain
40	chr1:154197600-154204400	Strong transcription	HSMM	muscle
41	chr1:154197600-154204600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:154197600-154205200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:154197600-154205400	Strong transcription	Fetal Lung	lung
44	chr1:154197600-154205800	Strong transcription	Rectal Smooth Muscle	rectum
45	chr1:154197600-154208800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:154197600-154209600	Strong transcription	Fetal Intestine Small	intestine
47	chr1:154197600-154210600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:154197600-154211200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:154197600-154211200	Strong transcription	Lung	lung
50	chr1:154197600-154212800	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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