Variant report

Variant	rs13331769
Chromosome Location	chr16:77246218-77246219
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	POLR2A	chr16:77246016-77248008	A549	lung:	n/a	n/a
2	POLR2A	chr16:77245941-77247081	HEK293	kidney:	n/a	n/a
3	SIN3AK20	chr16:77245966-77246566	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr16:77245882-77246578	GM12892	blood:	n/a	n/a
5	TAF1	chr16:77245911-77247928	A549	lung:	n/a	n/a
6	POLR2A	chr16:77246071-77246589	Raji	blood:	n/a	n/a
7	JUND	chr16:77245976-77246284	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr16:77245910-77246546	GM12878	blood:	n/a	n/a
9	MTA3	chr16:77246183-77246672	GM12878	blood:	n/a	n/a
10	EBF1	chr16:77246078-77246455	GM12878	blood:	n/a	n/a
11	MYC	chr16:77246131-77246331	K562	blood:	n/a	n/a
12	KAP1	chr16:77245907-77246273	U2OS	brain:	n/a	n/a
13	JUND	chr16:77246188-77246379	K562	blood:	n/a	n/a
14	TAF1	chr16:77246032-77246435	PFSK-1	brain:	n/a	n/a
15	EGR1	chr16:77245956-77246481	K562	blood:	n/a	chr16:77246281-77246294 chr16:77246114-77246124 chr16:77246163-77246173
16	CTCF	chr16:77246120-77246270	K562	blood:	n/a	n/a
17	POLR2A	chr16:77245886-77246536	SK-N-SH	brain:	n/a	n/a
18	ZBTB7A	chr16:77245881-77246937	ECC-1	luminal epithelium:	n/a	n/a
19	HA-E2F1	chr16:77245792-77246461	MCF-7	breast:	n/a	chr16:77246335-77246344
20	MAX	chr16:77245904-77247126	SK-N-SH	brain:	n/a	chr16:77246597-77246607 chr16:77246115-77246125
21	CTCF	chr16:77246139-77246218	Pancreas_OC	pancreas:	n/a	n/a
22	NRF1	chr16:77246082-77246267	GM12878	blood:	n/a	chr16:77246115-77246124
23	STAT1	chr16:77246039-77246301	GM12878	blood:	n/a	chr16:77246274-77246286 chr16:77246273-77246285 chr16:77246269-77246281
24	CTCF	chr16:77246080-77246230	GM12866	blood:	n/a	n/a
25	EGR1	chr16:77245690-77247060	HCT-116	colon:	n/a	chr16:77246281-77246294 chr16:77246562-77246572 chr16:77246114-77246124 chr16:77246163-77246173
26	POLR2A	chr16:77246029-77246473	MCF-7	breast:	n/a	n/a
27	REST	chr16:77245809-77246517	PFSK-1	brain:	n/a	n/a
28	CTCF	chr16:77246080-77246230	NHEK	skin:	n/a	n/a
29	TCF3	chr16:77246017-77246296	GM12878	blood:	n/a	chr16:77246105-77246118
30	HEY1	chr16:77246053-77246372	K562	blood:	n/a	chr16:77246140-77246155 chr16:77246332-77246347
31	TCF12	chr16:77245897-77246382	H1-hESC	embryonic stem cell:	n/a	n/a
32	EGR1	chr16:77246013-77246404	GM12878	blood:	n/a	chr16:77246281-77246294 chr16:77246114-77246124 chr16:77246163-77246173
33	CTCF	chr16:77246200-77246350	GM12868	blood:	n/a	n/a
34	PML	chr16:77245941-77246617	GM12878	blood:	n/a	n/a
35	EP300	chr16:77245892-77246332	H1-hESC	embryonic stem cell:	n/a	n/a
36	UBTF	chr16:77245963-77247079	K562	blood:	n/a	n/a
37	EBF1	chr16:77245990-77246389	GM12878	blood:	n/a	n/a
38	MAZ	chr16:77245924-77247050	GM12878	blood:	n/a	chr16:77246597-77246607 chr16:77246115-77246125
39	POLR2A	chr16:77246091-77246262	HepG2	liver:	n/a	n/a
40	CTCF	chr16:77246120-77246270	HCT-116	colon:	n/a	n/a
41	CTCF	chr16:77246174-77246263	H1-hESC	embryonic stem cell:	n/a	n/a
42	YY1	chr16:77245859-77246569	A549	lung:	n/a	chr16:77246147-77246158 chr16:77246302-77246313 chr16:77246309-77246318
43	YY1	chr16:77246001-77246520	GM12892	blood:	n/a	chr16:77246147-77246158 chr16:77246302-77246313 chr16:77246309-77246318
44	BHLHE40	chr16:77246069-77246442	GM12878	blood:	n/a	n/a
45	RCOR1	chr16:77245971-77247052	K562	blood:	n/a	n/a
46	EGR1	chr16:77245975-77246554	H1-hESC	embryonic stem cell:	n/a	chr16:77246281-77246294 chr16:77246114-77246124 chr16:77246163-77246173
47	SP1	chr16:77245631-77248366	HCT-116	colon:	n/a	chr16:77246115-77246125 chr16:77245959-77245971 chr16:77247070-77247079 chr16:77246122-77246131 chr16:77246336-77246348 chr16:77245964-77245976 chr16:77246118-77246132 chr16:77246114-77246126 chr16:77246115-77246124 chr16:77246338-77246347 chr16:77246561-77246573 chr16:77245966-77245975 chr16:77246982-77246994 chr16:77246203-77246214 chr16:77245959-77245971 chr16:77246596-77246608 chr16:77245964-77245976 chr16:77246558-77246572 chr16:77246562-77246571 chr16:77246982-77246994 chr16:77247069-77247078 chr16:77246336-77246348 chr16:77245961-77245970 chr16:77246337-77246346 chr16:77246983-77246993 chr16:77246561-77246573 chr16:77245960-77245969 chr16:77246114-77246126 chr16:77246563-77246572 chr16:77246116-77246125 chr16:77246738-77246747 chr16:77246291-77246305
48	POLR2A	chr16:77245904-77246540	U87	brain:	n/a	n/a
49	CTCF	chr16:77246200-77246350	GM12875	blood:	n/a	n/a
50	YY1	chr16:77246009-77246563	ECC-1	luminal epithelium:	n/a	chr16:77246147-77246158 chr16:77246302-77246313 chr16:77246309-77246318

No.	Distal block	Cell Line	Cell type
1	chr16:77224814..77227187-chr16:77245098..77247161,3	K562	blood:
2	chr16:77223598..77226407-chr16:77245076..77246907,2	MCF-7	breast:
3	chr16:77223923..77226639-chr16:77244818..77248823,8	K562	blood:

Variant related genes	Relation type
SYCE1L	TF binding region
ENSG00000103111	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2343037	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2343038	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343039	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887895	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71380947	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7196424	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9933644	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933799	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065343	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv542965	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13331769	SYCE1L	cis	Skin Sun Exposed Lower leg	GTEx
rs13331769	SYCE1L	cis	Whole Blood	GTEx
rs13331769	SYCE1L	cis	Thyroid	GTEx
rs13331769	SYCE1L	cis	Artery Tibial	GTEx
rs13331769	SYCE1L	cis	Nerve Tibial	GTEx
rs13331769	SYCE1L	cis	Adipose Subcutaneous	GTEx
rs13331769	SYCE1L	cis	Esophagus Muscularis	GTEx
rs13331769	SYCE1L	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77227200-77247200	Weak transcription	Hela-S3	cervix
2	chr16:77245400-77247200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr16:77245600-77246400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:77245600-77246400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr16:77245600-77246400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
6	chr16:77245600-77246800	Flanking Bivalent TSS/Enh	HepG2	liver
7	chr16:77245600-77247200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr16:77245600-77247200	Active TSS	Brain Germinal Matrix	brain
9	chr16:77245600-77247400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr16:77245600-77247400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr16:77245800-77246400	Flanking Active TSS	HMEC	breast
12	chr16:77245800-77246600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr16:77245800-77246600	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr16:77245800-77246600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr16:77245800-77246600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:77245800-77246600	Active TSS	Colonic Mucosa	Colon
17	chr16:77245800-77246600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
18	chr16:77245800-77246800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:77245800-77247000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr16:77245800-77247000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:77245800-77247000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr16:77245800-77247000	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr16:77245800-77247000	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr16:77245800-77247000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr16:77245800-77247000	Bivalent/Poised TSS	Fetal Stomach	stomach
26	chr16:77245800-77247200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr16:77245800-77247200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr16:77245800-77247200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:77245800-77247200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr16:77245800-77247200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr16:77245800-77247200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr16:77245800-77247200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr16:77245800-77247200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:77245800-77247200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr16:77245800-77247200	Active TSS	Brain Anterior Caudate	brain
36	chr16:77245800-77247200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr16:77245800-77247200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr16:77245800-77247200	Active TSS	Fetal Brain Female	brain
39	chr16:77245800-77247200	Active TSS	Ovary	ovary
40	chr16:77245800-77247200	Active TSS	Psoas Muscle	Psoas
41	chr16:77245800-77247200	Active TSS	Rectal Smooth Muscle	rectum
42	chr16:77245800-77247200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
43	chr16:77245800-77247200	Active TSS	HSMM	muscle
44	chr16:77245800-77247200	Active TSS	NHEK	skin
45	chr16:77245800-77247400	Active TSS	H9 Cell Line	embryonic stem cell
46	chr16:77245800-77247400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr16:77245800-77247400	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr16:77245800-77247400	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr16:77245800-77247400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr16:77245800-77247400	Active TSS	Primary T cells from cord blood	blood

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