Variant report

Variant	rs13438048
Chromosome Location	chr7:56161138-56161139
allele	C/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	POLR2A	chr7:56160798-56161301	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:56159355-56161778	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:56160453-56161157	K562	blood:	n/a	n/a
4	POLR2A	chr7:56160471-56161825	IMR90	lung:	n/a	n/a
5	POLR2A	chr7:56160376-56161357	K562	blood:	n/a	n/a
6	POLR2A	chr7:56160557-56162070	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr7:56160592-56161377	MCF-7	breast:	n/a	n/a
8	POLR2A	chr7:56160636-56161551	SK-N-MC	brain:	n/a	n/a
9	CTCF	chr7:56161080-56161230	HCM	heart:	n/a	n/a
10	POLR2A	chr7:56160367-56161618	HepG2	liver:	n/a	n/a
11	POLR2A	chr7:56160354-56161226	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr7:56160435-56161753	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr7:56159218-56162136	K562	blood:	n/a	n/a
14	POLR2A	chr7:56160286-56161560	A549	lung:	n/a	n/a
15	POLR2A	chr7:56160279-56161219	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr7:56160935-56161306	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56153997..56155986-chr7:56159698..56162469,2	K562	blood:
2	chr7:56158331..56162402-chr7:56164304..56169225,5	K562	blood:

Variant related genes	Relation type
PHKG1	TF binding region
ENSG00000238673	Chromatin interaction
ENSG00000164776	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10265826	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10274148	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10800	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12154781	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12155441	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12536548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12537948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12668193	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12671494	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12673255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014042	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242509	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270244	0.81[AFR][1000 genomes]
rs28438587	0.86[AMR][1000 genomes]
rs28558245	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778867	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3813505	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4345511	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4424212	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4427122	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4585698	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55940597	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56355538	0.82[AFR][1000 genomes]
rs58251663	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59723101	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6947671	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6960348	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6970842	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6971804	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140779	0.86[AFR][1000 genomes]
rs73140793	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73140794	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs766334	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7793536	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7793614	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats 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	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13438048	SUMF2	cis	Esophagus Muscularis	GTEx
rs13438048	SUMF2	cis	Whole Blood	GTEx
rs13438048	SUMF2	cis	lung	GTEx
rs13438048	SUMF2	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
3	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:56142000-56168000	Weak transcription	GM12878-XiMat	blood
5	chr7:56142200-56167800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:56146000-56167800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:56147000-56167400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:56147400-56167000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr7:56147400-56169800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:56147600-56167200	Weak transcription	HMEC	breast
11	chr7:56147600-56167400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:56147800-56164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:56147800-56167200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr7:56147800-56167400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:56148000-56165600	Weak transcription	Primary B cells from cord blood	blood
16	chr7:56148000-56167200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:56148800-56167400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:56149600-56167200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:56149800-56167600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:56149800-56168000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:56150000-56164000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:56150000-56166200	Weak transcription	Fetal Thymus	thymus
23	chr7:56150000-56166400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr7:56150400-56164000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:56152000-56167400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:56155600-56164000	Weak transcription	Dnd41	blood
27	chr7:56155600-56164200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:56155600-56165200	Weak transcription	Thymus	Thymus
29	chr7:56155600-56166000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:56155600-56167200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr7:56155600-56167400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr7:56155600-56167600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:56155800-56165400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr7:56155800-56167000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr7:56156000-56166200	Weak transcription	Fetal Intestine Large	intestine
36	chr7:56156800-56165200	Weak transcription	Fetal Brain Female	brain
37	chr7:56156800-56167000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr7:56156800-56167400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr7:56157000-56165400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr7:56157200-56165000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:56157800-56161200	Enhancers	Left Ventricle	heart
42	chr7:56157800-56167600	Weak transcription	K562	blood
43	chr7:56158200-56173200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:56158400-56167000	Weak transcription	Primary T cells from cord blood	blood
45	chr7:56158600-56164000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr7:56158800-56161200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr7:56159000-56161400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr7:56159200-56161200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr7:56159200-56161200	Enhancers	Fetal Lung	lung
50	chr7:56159200-56161400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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