Variant report

Variant	rs4885349
Chromosome Location	chr13:76358364-76358365
allele	A/C
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	EP300	chr13:76358054-76358643	SK-N-SH_RA	brain:	n/a	n/a
2	TFAP2A	chr13:76357734-76358536	Hela-S3	cervix:	n/a	chr13:76358219-76358234
3	SMC3	chr13:76358133-76358546	Hela-S3	cervix:	n/a	n/a
4	USF2	chr13:76358187-76358459	Hela-S3	cervix:	n/a	n/a
5	EP300	chr13:76357710-76359328	SK-N-SH	brain:	n/a	chr13:76357994-76358004 chr13:76357888-76357898
6	MXI1	chr13:76358298-76358379	Hela-S3	cervix:	n/a	n/a
7	GTF2F1	chr13:76358211-76358441	Hela-S3	cervix:	n/a	n/a
8	NR2F2	chr13:76358054-76358574	MCF-7	breast:	n/a	n/a
9	GATA2	chr13:76357964-76358603	SH-SY5Y	brain:	n/a	n/a
10	EP300	chr13:76358114-76358752	Hela-S3	cervix:	n/a	n/a
11	GATA3	chr13:76357896-76358499	SH-SY5Y	brain:	n/a	n/a
12	GATA3	chr13:76358093-76358697	SK-N-SH	brain:	n/a	n/a
13	TCF7L2	chr13:76358026-76358596	Hela-S3	cervix:	n/a	n/a
14	NFIC	chr13:76358102-76358705	SK-N-SH	brain:	n/a	n/a
15	TFAP2C	chr13:76357911-76358569	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr13:76357210-76358659	Hela-S3	cervix:	n/a	chr13:76357418-76357429 chr13:76357353-76357366 chr13:76357417-76357430 chr13:76357417-76357428 chr13:76357417-76357428 chr13:76357417-76357430
17	MAFK	chr13:76358240-76358559	Hela-S3	cervix:	n/a	n/a
18	MAX	chr13:76358108-76358472	Hela-S3	cervix:	n/a	n/a
19	EP300	chr13:76358113-76358521	SK-N-SH_RA	brain:	n/a	n/a
20	TCF12	chr13:76357734-76358543	A549	lung:	n/a	chr13:76357888-76357897
21	RFX5	chr13:76358115-76358672	Hela-S3	cervix:	n/a	n/a
22	NR2F2	chr13:76357922-76358550	MCF-7	breast:	n/a	n/a
23	PRDM1	chr13:76357963-76358497	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr13:76357975-76358630	MCF-7	breast:	n/a	n/a
25	RCOR1	chr13:76358050-76358589	Hela-S3	cervix:	n/a	n/a
26	MAZ	chr13:76358158-76358416	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
LMO7	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1036869	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1570556	0.89[ASN][1000 genomes]
rs2120067	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2120068	0.81[EUR][1000 genomes]
rs2274062	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4885348	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs618930	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7320216	0.84[LWK][hapmap];0.81[MKK][hapmap]
rs7320900	0.81[EUR][1000 genomes]
rs7321748	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7326714	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7331429	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7991448	0.86[LWK][hapmap]
rs7992526	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7996791	0.85[CEU][hapmap]
rs9530473	0.84[CEU][hapmap];0.83[GIH][hapmap]
rs9544043	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9573658	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9573659	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4885349	C13orf45	cis	Nerve Tibial	GTEx
rs4885349	TBC1D4	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76338000-76362800	Weak transcription	Fetal Stomach	stomach
2	chr13:76338800-76371000	Weak transcription	Fetal Thymus	thymus
3	chr13:76340000-76363600	Weak transcription	Thymus	Thymus
4	chr13:76343400-76370800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr13:76346800-76361600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr13:76347400-76361400	Weak transcription	HMEC	breast
7	chr13:76347800-76361400	Weak transcription	Gastric	stomach
8	chr13:76350000-76371000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr13:76350600-76361200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr13:76351400-76360200	Weak transcription	Right Ventricle	heart
11	chr13:76353400-76362800	Weak transcription	Lung	lung
12	chr13:76353400-76370600	Weak transcription	Primary T cells from cord blood	blood
13	chr13:76355200-76362400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr13:76355600-76370800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr13:76357000-76358400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr13:76357000-76358400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:76357000-76360200	Weak transcription	Left Ventricle	heart
18	chr13:76357000-76361400	Weak transcription	NH-A	brain
19	chr13:76357000-76362400	Weak transcription	Esophagus	oesophagus
20	chr13:76357000-76362800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:76357000-76363000	Weak transcription	Fetal Kidney	kidney
22	chr13:76357000-76368400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr13:76357200-76359600	Enhancers	Hela-S3	cervix
24	chr13:76357200-76360000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:76357200-76363000	Weak transcription	Brain Anterior Caudate	brain
26	chr13:76357400-76358400	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr13:76357400-76358400	Enhancers	Pancreas	Pancrea
28	chr13:76357400-76358600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:76357400-76359000	Enhancers	Fetal Intestine Small	intestine
30	chr13:76357400-76360400	Enhancers	Liver	Liver
31	chr13:76357600-76358400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr13:76357600-76358400	Enhancers	NHLF	lung
33	chr13:76357600-76358600	Enhancers	Fetal Intestine Large	intestine
34	chr13:76357600-76358800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:76357600-76360400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr13:76357800-76358600	Enhancers	Fetal Lung	lung
37	chr13:76357800-76358800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr13:76357800-76358800	Enhancers	Stomach Mucosa	stomach
39	chr13:76357800-76360200	Weak transcription	Right Atrium	heart
40	chr13:76357800-76362800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:76357800-76363000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr13:76358000-76358400	Enhancers	Ovary	ovary
43	chr13:76358000-76358400	Enhancers	Psoas Muscle	Psoas
44	chr13:76358000-76358400	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr13:76358000-76358400	Enhancers	Small Intestine	intestine
46	chr13:76358000-76358400	Flanking Active TSS	A549	lung
47	chr13:76358000-76358600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr13:76358000-76358600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr13:76358000-76358800	Enhancers	HSMMtube	muscle
50	chr13:76358000-76358800	Weak transcription	NHDF-Ad	bronchial

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