Variant report

Variant	rs10908739
Chromosome Location	chr1:154160655-154160656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154159154..154160815-chr1:154163047..154164875,2	MCF-7	breast:
2	chr1:154158539..154161524-chr1:154242189..154245561,3	MCF-7	breast:
3	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
4	chr1:154158467..154161316-chr1:154169815..154172829,3	MCF-7	breast:
5	chr1:154129855..154131682-chr1:154158722..154160655,2	K562	blood:
6	chr1:154159712..154161711-chr1:154198727..154200350,2	K562	blood:
7	chr1:153963252..153965177-chr1:154158511..154161067,3	MCF-7	breast:
8	chr1:154158424..154161181-chr1:154245114..154247197,2	MCF-7	breast:
9	chr1:154155288..154157675-chr1:154160593..154163426,2	K562	blood:
10	chr1:154156233..154161758-chr1:154162933..154167291,6	K562	blood:
11	chr1:154159143..154160750-chr1:154457957..154460845,2	MCF-7	breast:
12	chr1:153963118..153965520-chr1:154159636..154162394,3	K562	blood:
13	chr1:154158089..154161877-chr1:154191453..154195317,5	K562	blood:
14	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169291	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10797058	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10797061	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10908751	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11265285	0.84[EUR][1000 genomes]
rs1194580	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1194582	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1194599	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1194600	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1194602	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1194603	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1194604	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12044616	0.89[EUR][1000 genomes]
rs12063830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095767	0.85[EUR][1000 genomes]
rs2220390	0.84[EUR][1000 genomes]
rs2790690	1.00[JPT][hapmap]
rs3001363	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4072431	0.82[CEU][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4364874	0.82[CEU][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4393149	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4400599	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4540651	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4579747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845364	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845609	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4845610	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6680947	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7516809	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7521047	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7526644	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7533952	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7537213	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9803862	0.89[EUR][1000 genomes]
rs9804045	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9943097	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	esv3453084	chr1:154156328-154161626	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv3453085	chr1:154156328-154161626	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	esv12863	chr1:154158242-154161302	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10908739	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154156200-154163000	Weak transcription	Psoas Muscle	Psoas
2	chr1:154156400-154163200	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:154156400-154164200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:154156600-154164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:154156800-154164200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:154157200-154164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:154158800-154160800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
8	chr1:154159000-154164600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:154159000-154184400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:154159600-154160800	Enhancers	Pancreas	Pancrea
11	chr1:154159600-154162800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:154159600-154162800	Weak transcription	Hela-S3	cervix
13	chr1:154159600-154163000	Weak transcription	HSMM	muscle
14	chr1:154159600-154163200	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr1:154159800-154160800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:154159800-154162600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:154160000-154160800	Enhancers	K562	blood
18	chr1:154160200-154160800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:154160200-154162800	Weak transcription	HepG2	liver
20	chr1:154160200-154164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:154160400-154161000	Weak transcription	Right Atrium	heart
22	chr1:154160400-154169400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:154160600-154162800	Weak transcription	HSMMtube	muscle
24	chr1:154160600-154163000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:154160600-154164400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:154160600-154164400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:154160600-154164600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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