Variant report

Variant	rs4393149
Chromosome Location	chr1:154195753-154195754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:154194477-154196011	K562	blood:	n/a	n/a
2	SETDB1	chr1:154195040-154195825	U2OS	brain:	n/a	n/a
3	POLR2A	chr1:154191381-154195966	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:154195513-154196668	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:154195548-154196373	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:154194303..154196479-chr1:154230537..154232056,2	MCF-7	breast:
2	chr1:153916668..153920266-chr1:154191885..154196472,6	MCF-7	breast:
3	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
4	chr1:154193867..154196410-chr1:154304631..154306238,2	K562	blood:
5	chr1:154161421..154168420-chr1:154191340..154198003,13	MCF-7	breast:
6	chr1:154151605..154157694-chr1:154191153..154195788,18	MCF-7	breast:
7	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
8	chr1:154190796..154197109-chr1:154207892..154217963,21	MCF-7	breast:
9	chr1:153961938..153967162-chr1:154189861..154195978,9	K562	blood:
10	chr1:154195648..154197587-chr1:154233739..154236534,2	MCF-7	breast:
11	chr1:154177747..154182716-chr1:154190412..154196946,9	K562	blood:
12	chr1:154194086..154195833-chr1:154296026..154297621,2	K562	blood:
13	chr1:154171859..154174380-chr1:154194428..154197108,2	MCF-7	breast:
14	chr1:154194086..154195906-chr1:154295331..154297621,3	K562	blood:

No data

Variant related genes	Relation type
UBAP2L	TF binding region
C1orf43	TF binding region
ENSG00000143569	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000163263	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000198837	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10797058	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10797061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908739	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265285	0.88[EUR][1000 genomes]
rs1194580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194582	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194599	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194603	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044616	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063830	1.00[ASW][hapmap];0.87[GIH][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12095767	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12354278	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13796	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1591902	1.00[CHB][hapmap]
rs1832582	1.00[JPT][hapmap]
rs2220390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790686	0.82[CHB][hapmap]
rs2841108	0.82[CHB][hapmap]
rs3001365	0.82[CHB][hapmap]
rs4072431	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4364874	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4579747	1.00[ASW][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845364	0.86[ASW][hapmap]
rs4845605	1.00[ASW][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs4845609	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807361	0.85[ASN][1000 genomes]
rs6667222	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6680947	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7516809	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7526644	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533952	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9803862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943097	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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
rs4393149	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	chr1:154192200-154195800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:154194400-154195800	Flanking Active TSS	HUVEC	blood vessel
3	chr1:154194400-154195800	Transcr. at gene 5' and 3'	K562	blood
4	chr1:154194400-154196000	Flanking Active TSS	Dnd41	blood
5	chr1:154194400-154197400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:154194400-154197600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:154194600-154196200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr1:154194600-154196600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:154194600-154196600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:154194600-154197200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:154194600-154197400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:154194600-154197600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:154194600-154197600	Weak transcription	Gastric	stomach
14	chr1:154194600-154197600	Weak transcription	Spleen	Spleen
15	chr1:154194600-154199600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:154194600-154201000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:154194600-154201000	Weak transcription	Aorta	Aorta
18	chr1:154194600-154201000	Weak transcription	Esophagus	oesophagus
19	chr1:154194600-154201000	Weak transcription	Pancreas	Pancrea
20	chr1:154194800-154195800	Enhancers	Stomach Mucosa	stomach
21	chr1:154194800-154196000	Enhancers	Primary B cells from cord blood	blood
22	chr1:154194800-154197600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:154194800-154197600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:154194800-154197600	Weak transcription	Lung	lung
25	chr1:154194800-154197800	Weak transcription	Placenta	Placenta
26	chr1:154194800-154197800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:154194800-154198000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:154194800-154198600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:154194800-154199200	Weak transcription	Left Ventricle	heart
30	chr1:154194800-154199400	Weak transcription	Small Intestine	intestine
31	chr1:154194800-154202000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:154195000-154195800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:154195000-154195800	Enhancers	Fetal Lung	lung
34	chr1:154195000-154196200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:154195000-154196200	Enhancers	Fetal Brain Male	brain
36	chr1:154195000-154196200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:154195000-154196200	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:154195000-154196400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr1:154195000-154196400	Enhancers	Fetal Heart	heart
40	chr1:154195000-154196800	Enhancers	Fetal Intestine Large	intestine
41	chr1:154195000-154197000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:154195000-154197000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr1:154195000-154197000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr1:154195000-154197200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:154195000-154197800	Weak transcription	Brain Substantia Nigra	brain
46	chr1:154195200-154195800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:154195200-154195800	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:154195200-154195800	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr1:154195200-154196200	Enhancers	Brain Germinal Matrix	brain
50	chr1:154195200-154196200	Enhancers	Fetal Intestine Small	intestine

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