Variant report

Variant	rs1057478
Chromosome Location	chr13:53226118-53226119
allele	C/T
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	GABPA	chr13:53225956-53227387	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr13:53226079-53227507	GM15510	blood:	n/a	n/a
3	CHD1	chr13:53225239-53227799	H1-hESC	embryonic stem cell:	n/a	chr13:53227757-53227764
4	POLR2A	chr13:53225861-53227353	HUVEC	blood vessel:	n/a	n/a
5	MXI1	chr13:53225750-53227564	IMR90	lung:	n/a	n/a
6	GTF2F1	chr13:53226058-53227390	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr13:53225876-53227475	GM12892	blood:	n/a	n/a
8	TBL1XR1	chr13:53225985-53227635	GM12878	blood:	n/a	n/a
9	ELF1	chr13:53226004-53227319	MCF-7	breast:	n/a	chr13:53226444-53226453
10	GABPA	chr13:53226064-53227241	A549	lung:	n/a	n/a
11	YY1	chr13:53226085-53227452	ECC-1	luminal epithelium:	n/a	n/a
12	CREB1	chr13:53226061-53227272	HepG2	liver:	n/a	n/a
13	RCOR1	chr13:53226022-53227098	K562	blood:	n/a	n/a
14	MYC	chr13:53226078-53227329	A549	lung:	n/a	chr13:53226741-53226750
15	ZMIZ1	chr13:53226058-53227570	K562	blood:	n/a	n/a
16	MAX	chr13:53226007-53227256	H1-hESC	embryonic stem cell:	n/a	chr13:53226741-53226750
17	MAX	chr13:53225969-53227165	H1-hESC	embryonic stem cell:	n/a	chr13:53226741-53226750
18	MYC	chr13:53226021-53227257	K562	blood:	n/a	chr13:53226741-53226750
19	RELA	chr13:53226099-53227482	GM18951	blood:	n/a	n/a
20	CREB1	chr13:53226067-53227275	HepG2	liver:	n/a	n/a
21	POLR2A	chr13:53225967-53227657	K562	blood:	n/a	n/a
22	MAX	chr13:53226104-53227333	K562	blood:	n/a	chr13:53226741-53226750
23	CTCF	chr13:53225864-53227462	A549	lung:	n/a	n/a
24	STAT5A	chr13:53226078-53227415	GM12878	blood:	n/a	chr13:53226440-53226460 chr13:53226758-53226766
25	EP300	chr13:53226090-53227222	GM12878	blood:	n/a	chr13:53227101-53227115 chr13:53226444-53226451
26	YY1	chr13:53226110-53227285	GM12878	blood:	n/a	n/a
27	POLR2A	chr13:53226000-53227372	K562	blood:	n/a	n/a
28	REST	chr13:53226074-53226631	SK-N-SH	brain:	n/a	chr13:53226171-53226179
29	SP1	chr13:53226106-53227296	A549	lung:	n/a	chr13:53226805-53226814 chr13:53226804-53226816 chr13:53226806-53226815 chr13:53226806-53226815
30	TAF1	chr13:53226069-53227233	A549	lung:	n/a	n/a
31	MAZ	chr13:53226025-53227297	Hela-S3	cervix:	n/a	chr13:53226741-53226750
32	MYC	chr13:53225567-53227156	MCF10A-Er-Src	breast:	n/a	chr13:53226741-53226750
33	KAT2A	chr13:53226086-53226978	Hela-S3	cervix:	n/a	n/a
34	FOXM1	chr13:53225997-53227623	GM12878	blood:	n/a	n/a
35	TAF1	chr13:53226109-53227225	GM12891	blood:	n/a	n/a
36	TEAD4	chr13:53226040-53227273	ECC-1	luminal epithelium:	n/a	n/a
37	MAX	chr13:53226056-53227209	HepG2	liver:	n/a	chr13:53226741-53226750
38	GATA3	chr13:53226098-53227136	A549	lung:	n/a	chr13:53226567-53226575
39	ELF1	chr13:53226096-53227431	GM12878	blood:	n/a	chr13:53226444-53226453
40	TAF1	chr13:53226114-53227145	GM12892	blood:	n/a	n/a
41	POLR2A	chr13:53226008-53227459	H1-hESC	embryonic stem cell:	n/a	n/a
42	TEAD4	chr13:53226068-53226793	K562	blood:	n/a	n/a
43	E2F6	chr13:53226092-53226592	K562	blood:	n/a	n/a
44	E2F6	chr13:53226049-53226488	K562	blood:	n/a	n/a
45	POLR2A	chr13:53225676-53227735	IMR90	lung:	n/a	n/a
46	MYC	chr13:53226100-53227167	K562	blood:	n/a	chr13:53226741-53226750
47	TAF1	chr13:53226009-53227271	ECC-1	luminal epithelium:	n/a	n/a
48	MXI1	chr13:53226090-53227518	HepG2	liver:	n/a	n/a
49	POLR2A	chr13:53226087-53227163	H1-hESC	embryonic stem cell:	n/a	n/a
50	TBP	chr13:53226049-53227513	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:53189348..53193688-chr13:53225267..53228139,8	MCF-7	breast:
2	chr13:53190009..53193421-chr13:53225046..53226798,3	K562	blood:
3	chr13:53191451..53193324-chr13:53224550..53227605,3	MCF-7	breast:
4	chr13:53223315..53224976-chr13:53225042..53226635,2	MCF-7	breast:
5	chr13:53226033..53226915-chr3:101568139..101568761,2	Hela-S3	cervix:
6	chr13:53225264..53227638-chr2:38976930..38979242,2	MCF-7	breast:
7	chr13:53225937..53226845-chr6:26056295..26057101,2	NB4	blood:
8	chr13:53023588..53025754-chr13:53225469..53228375,2	K562	blood:
9	chr13:53199936..53201723-chr13:53223791..53226214,2	K562	blood:
10	chr13:53225894..53226531-chr17:37356466..37357068,2	Hela-S3	cervix:
11	chr13:53217025..53220829-chr13:53221987..53226213,6	K562	blood:

Variant related genes	Relation type
SUGT1	TF binding region
ENSG00000144802	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000139675	Chromatin interaction
ENSG00000136100	Chromatin interaction
ENSG00000250299	Chromatin interaction
ENSG00000108298	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000187837	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11616261	0.87[AFR][1000 genomes]
rs11616459	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11618716	0.90[ASW][hapmap];0.89[MKK][hapmap]
rs1924036	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2038826	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2147676	0.83[CHB][hapmap]
rs2147692	1.00[ASW][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs2575960	0.85[CHB][hapmap]
rs2760815	0.91[CEU][hapmap]
rs3742297	1.00[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs3892337	0.81[YRI][hapmap]
rs4284531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4884235	0.85[CHB][hapmap]
rs61959657	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7139495	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap]
rs7139630	0.85[CHB][hapmap]
rs7328729	0.85[CHB][hapmap]
rs7334137	0.85[CHB][hapmap]
rs7334677	0.85[CHB][hapmap]
rs7336771	0.85[CHB][hapmap]
rs9526950	0.84[ASN][1000 genomes]
rs9526968	0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap]
rs9526974	0.90[ASW][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs9526975	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9526979	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9536079	0.89[ASW][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.81[YRI][hapmap]
rs9536104	0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[MKK][hapmap]
rs9536123	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs9536185	0.95[ASN][1000 genomes]
rs9536190	0.95[ASN][1000 genomes]
rs9536199	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9536204	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536211	0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9536212	0.93[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs9536219	0.90[ASW][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs9536220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536242	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9536262	1.00[ASW][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.91[MKK][hapmap];0.84[YRI][hapmap]
rs9563113	0.85[CHB][hapmap]
rs9563114	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv820041	chr13:53061338-53280588	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv819201	chr13:53137490-53240330	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1037189	chr13:53173013-53287060	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv541775	chr13:53173013-53287060	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
13	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1057478	CKAP2	cis	cerebellum	SCAN
rs1057478	CKAP2	cis	parietal	SCAN
rs1057478	HNRNPA1L2	cis	cerebellum	SCAN
rs1057478	CKAP2	cis	Nerve Tibial	GTEx
rs1057478	CKAP2	cis	Thyroid	GTEx
rs1057478	LECT1	cis	parietal	SCAN
rs1057478	SUGT1	cis	cerebellum	SCAN
rs1057478	HNRNPA1L2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53224400-53227800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:53224400-53228600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr13:53224600-53228600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:53224600-53229200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:53224800-53226400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:53224800-53228400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr13:53225000-53227800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:53225000-53228000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr13:53225000-53228200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr13:53225000-53228200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:53225000-53228200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:53225000-53228200	Active TSS	NHDF-Ad	bronchial
13	chr13:53225000-53228400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr13:53225000-53228400	Active TSS	Fetal Intestine Small	intestine
15	chr13:53225000-53228600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr13:53225000-53228600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr13:53225000-53229000	Active TSS	K562	blood
18	chr13:53225000-53229400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:53225200-53226400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr13:53225200-53228000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:53225200-53228000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:53225200-53228000	Active TSS	Fetal Kidney	kidney
23	chr13:53225200-53228000	Active TSS	Fetal Stomach	stomach
24	chr13:53225200-53228200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:53225200-53228200	Active TSS	Colonic Mucosa	Colon
26	chr13:53225200-53228200	Active TSS	GM12878-XiMat	blood
27	chr13:53225200-53228200	Active TSS	HSMM	muscle
28	chr13:53225200-53228400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr13:53225200-53228400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:53225200-53228400	Active TSS	Fetal Intestine Large	intestine
31	chr13:53225200-53228400	Active TSS	Fetal Muscle Trunk	muscle
32	chr13:53225200-53228400	Active TSS	A549	lung
33	chr13:53225200-53228600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr13:53225200-53228600	Active TSS	Hela-S3	cervix
35	chr13:53225400-53226200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:53225400-53226200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr13:53225400-53226200	Weak transcription	Spleen	Spleen
38	chr13:53225400-53226600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr13:53225400-53227200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:53225400-53227200	Active TSS	HepG2	liver
41	chr13:53225400-53227600	Active TSS	Fetal Muscle Leg	muscle
42	chr13:53225400-53227600	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr13:53225400-53227800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr13:53225400-53227800	Active TSS	Brain Angular Gyrus	brain
45	chr13:53225400-53228000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:53225400-53228000	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr13:53225400-53228000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr13:53225400-53228000	Active TSS	Muscle Satellite Cultured Cells	--
49	chr13:53225400-53228000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr13:53225400-53228000	Active TSS	Fetal Brain Male	brain

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