Variant report

Variant	rs60610828
Chromosome Location	chr11:73999159-73999160
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	BCL3	chr11:73999067-73999676	A549	lung:	n/a	n/a
2	EP300	chr11:73999074-73999771	Hela-S3	cervix:	n/a	chr11:73999513-73999526 chr11:73999681-73999695
3	FOS	chr11:73999119-73999640	HUVEC	blood vessel:	n/a	chr11:73999409-73999421 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999409-73999420 chr11:73999411-73999419
4	NR3C1	chr11:73999107-73999684	A549	lung:	n/a	chr11:73999410-73999419 chr11:73999407-73999414
5	FOSL2	chr11:73999127-73999708	SK-N-SH	brain:	n/a	chr11:73999409-73999421 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999411-73999419
6	TCF12	chr11:73999124-73999576	A549	lung:	n/a	n/a
7	MAX	chr11:73999041-73999760	A549	lung:	n/a	n/a
8	GATA3	chr11:73999104-73999551	A549	lung:	n/a	n/a
9	EP300	chr11:73999054-73999780	SK-N-SH	brain:	n/a	chr11:73999513-73999526 chr11:73999681-73999695
10	EP300	chr11:73998909-73999803	A549	lung:	n/a	chr11:73999513-73999526 chr11:73999681-73999695
11	JUND	chr11:73999038-73999664	A549	lung:	n/a	chr11:73999409-73999421 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999411-73999419
12	RAD21	chr11:73999145-73999671	Hela-S3	cervix:	n/a	n/a
13	MAX	chr11:73998730-73999871	A549	lung:	n/a	n/a
14	GATA3	chr11:73998942-73999918	A549	lung:	n/a	n/a
15	GATA3	chr11:73999037-73999767	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr11:73999041-73999717	HUVEC	blood vessel:	n/a	n/a
17	SP1	chr11:73998976-73999784	A549	lung:	n/a	n/a
18	TCF12	chr11:73998911-73999894	A549	lung:	n/a	n/a
19	FOSL2	chr11:73998930-73999796	A549	lung:	n/a	chr11:73999409-73999421 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999411-73999419
20	SMC3	chr11:73999135-73999580	Hela-S3	cervix:	n/a	n/a
21	JUND	chr11:73999096-73999729	SK-N-SH	brain:	n/a	chr11:73999409-73999421 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999411-73999419
22	FOSL1	chr11:73999157-73999573	HCT-116	colon:	n/a	chr11:73999409-73999421 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999411-73999419
23	CEBPB	chr11:73999123-73999851	Hela-S3	cervix:	n/a	n/a
24	PBX3	chr11:73999086-73999802	SK-N-SH	brain:	n/a	n/a
25	REST	chr11:73999058-73999731	A549	lung:	n/a	n/a
26	TCF12	chr11:73999091-73999790	SK-N-SH	brain:	n/a	n/a
27	TBP	chr11:73999071-73999619	Hela-S3	cervix:	n/a	n/a
28	RCOR1	chr11:73999143-73999627	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr11:73999127-73999590	A549	lung:	n/a	n/a
30	FOXA2	chr11:73999033-73999718	A549	lung:	n/a	n/a
31	CEBPB	chr11:73999053-73999810	A549	lung:	n/a	n/a
32	RFX5	chr11:73999153-73999643	Hela-S3	cervix:	n/a	chr11:73999559-73999568
33	GABPA	chr11:73999095-73999645	A549	lung:	n/a	n/a
34	FOSL2	chr11:73999151-73999597	A549	lung:	n/a	chr11:73999409-73999421 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999410-73999420 chr11:73999411-73999419
35	MAX	chr11:73999152-73999820	Hela-S3	cervix:	n/a	n/a
36	GATA3	chr11:73999056-73999881	SK-N-SH	brain:	n/a	n/a
37	SP1	chr11:73998899-73999820	A549	lung:	n/a	n/a
38	POLR2A	chr11:73999157-73999487	HUVEC	blood vessel:	n/a	n/a
39	CTCF	chr11:73999100-73999250	HMF	breast:	n/a	n/a
40	NFIC	chr11:73999111-73999587	SK-N-SH	brain:	n/a	n/a
41	STAT3	chr11:73999154-73999663	Hela-S3	cervix:	n/a	n/a
42	TCF12	chr11:73998981-73999802	SK-N-SH	brain:	n/a	n/a
43	BCL3	chr11:73999042-73999798	A549	lung:	n/a	n/a
44	CHD2	chr11:73999148-73999598	Hela-S3	cervix:	n/a	n/a
45	EP300	chr11:73998970-73999764	A549	lung:	n/a	chr11:73999513-73999526 chr11:73999681-73999695
46	NFIC	chr11:73999038-73999864	SK-N-SH	brain:	n/a	n/a
47	GATA2	chr11:73999126-73999717	HUVEC	blood vessel:	n/a	n/a
48	PBX3	chr11:73999136-73999667	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
P4HA3	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11236056	1.00[ASN][1000 genomes]
rs11236057	1.00[ASN][1000 genomes]
rs12416880	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417457	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417458	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417835	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418387	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419385	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420538	1.00[ASN][1000 genomes]
rs12421564	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421595	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36014178	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57858196	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58030284	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58206408	1.00[ASN][1000 genomes]
rs58462364	1.00[ASN][1000 genomes]
rs58557652	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58587692	1.00[ASN][1000 genomes]
rs59325091	1.00[ASN][1000 genomes]
rs59749117	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59848587	1.00[ASN][1000 genomes]
rs60134332	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60721424	1.00[ASN][1000 genomes]
rs61026077	1.00[ASN][1000 genomes]
rs61109636	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60610828	PGM2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73990600-73999200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr11:73990600-73999400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:73992000-73999200	Weak transcription	Aorta	Aorta
4	chr11:73995200-73999200	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:73995400-73999200	Weak transcription	Stomach Mucosa	stomach
6	chr11:73996000-73999200	Weak transcription	NHDF-Ad	bronchial
7	chr11:73997200-73999800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:73997400-74000000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:73998400-73999200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:73998600-73999400	Enhancers	NHLF	lung
11	chr11:73998600-74000400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:73998800-73999800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:73998800-73999800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:73998800-74000000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:73998800-74000200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:73998800-74000200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr11:73999000-73999200	Flanking Active TSS	HUVEC	blood vessel
18	chr11:73999000-73999600	Flanking Active TSS	A549	lung
19	chr11:73999000-73999600	Flanking Active TSS	Hela-S3	cervix
20	chr11:73999000-73999800	Enhancers	Adipose Nuclei	Adipose
21	chr11:73999000-73999800	Enhancers	HSMM	muscle
22	chr11:73999000-73999800	Enhancers	NHEK	skin
23	chr11:73999000-74000400	Enhancers	NH-A	brain
24	chr11:73999000-74000400	Enhancers	Osteobl	bone

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