Variant report

Variant	rs1159278
Chromosome Location	chr13:98085349-98085350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr13:98084895-98085896	GM12878	blood:	n/a	chr13:98085678-98085690 chr13:98085658-98085668 chr13:98085638-98085647 chr13:98085678-98085690 chr13:98085636-98085648 chr13:98085636-98085648 chr13:98085417-98085438 chr13:98085635-98085642 chr13:98085286-98085307
2	MAZ	chr13:98084721-98086670	GM12878	blood:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085403-98085414 chr13:98085402-98085415
3	MAFF	chr13:98085154-98085564	HepG2	liver:	n/a	n/a
4	HEY1	chr13:98084947-98086322	HepG2	liver:	n/a	n/a
5	RFX5	chr13:98084880-98086464	Hela-S3	cervix:	n/a	chr13:98085517-98085531 chr13:98085516-98085531
6	MXI1	chr13:98085152-98086202	Hela-S3	cervix:	n/a	n/a
7	E2F6	chr13:98084761-98086194	H1-hESC	embryonic stem cell:	n/a	chr13:98086090-98086101 chr13:98085297-98085306 chr13:98085384-98085393
8	POLR2A	chr13:98084686-98087246	GM19193	blood:	n/a	n/a
9	PAX5	chr13:98084989-98085764	GM12878	blood:	n/a	n/a
10	CREB1	chr13:98085042-98086007	ECC-1	luminal epithelium:	n/a	n/a
11	RCOR1	chr13:98084635-98086504	IMR90	lung:	n/a	n/a
12	E2F6	chr13:98084954-98085798	H1-hESC	embryonic stem cell:	n/a	chr13:98085297-98085306 chr13:98085384-98085393
13	POLR2A	chr13:98084527-98087335	H1-hESC	embryonic stem cell:	n/a	n/a
14	NFIC	chr13:98085214-98085670	HepG2	liver:	n/a	n/a
15	POLR2A	chr13:98084760-98086269	SK-N-MC	brain:	n/a	n/a
16	MAFK	chr13:98084880-98086172	Hela-S3	cervix:	n/a	n/a
17	USF1	chr13:98085216-98085778	A549	lung:	n/a	n/a
18	POU2F2	chr13:98084875-98085750	GM12891	blood:	n/a	n/a
19	RELA	chr13:98084570-98086193	GM19099	blood:	n/a	n/a
20	FOXP2	chr13:98085088-98085852	SK-N-MC	brain:	n/a	n/a
21	YY1	chr13:98084850-98085788	ECC-1	luminal epithelium:	n/a	n/a
22	MXI1	chr13:98084803-98087739	IMR90	lung:	n/a	n/a
23	MYBL2	chr13:98085000-98085895	HepG2	liver:	n/a	n/a
24	FOXA1	chr13:98085348-98085669	T-47D	breast:	n/a	n/a
25	JUND	chr13:98085074-98085896	A549	lung:	n/a	chr13:98085565-98085579
26	POLR2A	chr13:98084848-98086280	GM12878	blood:	n/a	n/a
27	SRF	chr13:98085046-98085651	MCF-7	breast:	n/a	n/a
28	POLR2A	chr13:98084880-98086943	HL-60	blood:	n/a	n/a
29	USF1	chr13:98085159-98085742	A549	lung:	n/a	chr13:98085193-98085209
30	POLR2A	chr13:98084910-98086318	ECC-1	luminal epithelium:	n/a	n/a
31	SP2	chr13:98085095-98085664	HepG2	liver:	n/a	chr13:98085636-98085645
32	TEAD4	chr13:98085340-98085722	H1-hESC	embryonic stem cell:	n/a	n/a
33	ELF1	chr13:98084942-98085867	SK-N-SH	brain:	n/a	n/a
34	ZNF143	chr13:98085031-98086331	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr13:98084914-98087078	MCF-7	breast:	n/a	n/a
36	EP300	chr13:98085098-98085689	HepG2	liver:	n/a	n/a
37	POLR2A	chr13:98085028-98086290	HCT-116	colon:	n/a	n/a
38	BACH1	chr13:98085062-98085771	H1-hESC	embryonic stem cell:	n/a	n/a
39	IRF3	chr13:98084971-98085838	GM12878	blood:	n/a	chr13:98085678-98085692 chr13:98085636-98085650 chr13:98085384-98085393 chr13:98085297-98085306 chr13:98085657-98085671
40	POLR2A	chr13:98084907-98085877	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr13:98084510-98087400	GM19099	blood:	n/a	n/a
42	CREB1	chr13:98084926-98086607	HepG2	liver:	n/a	n/a
43	RCOR1	chr13:98085340-98086419	K562	blood:	n/a	n/a
44	SP1	chr13:98084810-98086002	A549	lung:	n/a	chr13:98085678-98085690 chr13:98085658-98085668 chr13:98085984-98085993 chr13:98085638-98085647 chr13:98085678-98085690 chr13:98085636-98085648 chr13:98085636-98085648 chr13:98085417-98085438 chr13:98085635-98085642 chr13:98085286-98085307
45	MAX	chr13:98084913-98086034	A549	lung:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
46	USF1	chr13:98085128-98085705	A549	lung:	n/a	chr13:98085193-98085209
47	MAX	chr13:98084810-98085722	H1-hESC	embryonic stem cell:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
48	POLR2A	chr13:98084869-98086906	A549	lung:	n/a	n/a
49	POLR2A	chr13:98084594-98086327	SK-N-SH	brain:	n/a	n/a
50	MYC	chr13:98085018-98086381	MCF10A-Er-Src	breast:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:98078675..98081221-chr13:98083499..98086151,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OXGR1-6	chr13:98081597-98086236	NONHSAT034832

Variant related genes	Relation type
RAP2A	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11616843	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12873919	0.81[LWK][hapmap];0.88[YRI][hapmap]
rs1304392	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1467693	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2389908	0.88[YRI][hapmap]
rs2389909	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2389910	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7322222	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[MEX][hapmap]
rs7328713	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9300410	0.88[CEU][hapmap]
rs9513245	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9516938	0.86[ASN][1000 genomes]
rs9554396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9634445	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv1791802	chr13:98076911-98096882	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1804050	chr13:98076911-98096882	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1794802	chr13:98076911-98106042	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv1797132	chr13:98076911-98106042	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv562794	chr13:98083262-98086828	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv562795	chr13:98084675-98086470	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
8	nsv562796	chr13:98085324-98086470	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
9	nsv562797	chr13:98085324-98086521	ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
10	esv1791968	chr13:98085324-98086828	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
11	esv1795003	chr13:98085324-98086828	Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
12	esv1796222	chr13:98085349-98086521	Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	esv1797121	chr13:98085349-98086777	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
14	esv1835247	chr13:98085349-98086777	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
15	esv1792667	chr13:98085349-98086828	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
16	esv1801896	chr13:98085349-98086828	Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
17	esv1836638	chr13:98085349-98086828	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:98083200-98088000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr13:98083400-98088800	Active TSS	GM12878-XiMat	blood
3	chr13:98083600-98088200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr13:98083800-98088600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr13:98083800-98089200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr13:98084000-98088000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:98084000-98088600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr13:98084000-98088800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr13:98084000-98088800	Active TSS	Fetal Kidney	kidney
10	chr13:98084000-98089200	Active TSS	NHLF	lung
11	chr13:98084200-98088000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:98084200-98088000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:98084200-98088000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:98084200-98088200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:98084200-98089000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:98084200-98089000	Active TSS	NHDF-Ad	bronchial
17	chr13:98084400-98087200	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr13:98084400-98087600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr13:98084400-98087600	Active TSS	A549	lung
20	chr13:98084400-98088000	Active TSS	Duodenum Mucosa	Duodenum
21	chr13:98084400-98088000	Active TSS	Rectal Smooth Muscle	rectum
22	chr13:98084400-98088200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:98084400-98088200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:98084400-98088400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:98084400-98088400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr13:98084400-98088400	Active TSS	Fetal Thymus	thymus
27	chr13:98084400-98088400	Active TSS	HSMM	muscle
28	chr13:98084400-98088600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr13:98084400-98088600	Active TSS	Fetal Muscle Leg	muscle
30	chr13:98084400-98088600	Active TSS	Fetal Stomach	stomach
31	chr13:98084400-98088800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr13:98084400-98088800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:98084400-98088800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr13:98084400-98088800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr13:98084400-98089000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr13:98084400-98089200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr13:98084400-98089200	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr13:98084400-98089600	Active TSS	Right Atrium	heart
39	chr13:98084600-98085400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr13:98084600-98087000	Active TSS	Brain Germinal Matrix	brain
41	chr13:98084600-98087400	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr13:98084600-98087400	Active TSS	Gastric	stomach
43	chr13:98084600-98087400	Active TSS	Placenta Amnion	Placenta Amnion
44	chr13:98084600-98087600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr13:98084600-98087600	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr13:98084600-98087600	Active TSS	Colon Smooth Muscle	Colon
47	chr13:98084600-98087600	ZNF genes & repeats	Fetal Brain Male	brain
48	chr13:98084600-98087600	Active TSS	Lung	lung
49	chr13:98084600-98087600	Active TSS	Psoas Muscle	Psoas
50	chr13:98084600-98087800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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