Variant report

Variant	rs1862043
Chromosome Location	chr12:50576316-50576317
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	RAD21	chr12:50576261-50576593	SK-N-SH_RA	brain:	n/a	chr12:50576426-50576445
2	SMC3	chr12:50576257-50576644	Hela-S3	cervix:	n/a	chr12:50576427-50576441
3	RAD21	chr12:50576222-50576657	ECC-1	luminal epithelium:	n/a	chr12:50576426-50576445
4	RAD21	chr12:50576210-50576716	HCT-116	colon:	n/a	chr12:50576426-50576445
5	CTCF	chr12:50576179-50576663	MCF-7	breast:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
6	RAD21	chr12:50576142-50576755	MCF-7	breast:	n/a	chr12:50576426-50576445
7	CTCF	chr12:50576132-50576689	HCT-116	colon:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
8	CTCF	chr12:50576261-50576604	GM12878	blood:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
9	RAD21	chr12:50576090-50576747	MCF-7	breast:	n/a	chr12:50576426-50576445
10	RAD21	chr12:50576260-50576643	Hela-S3	cervix:	n/a	chr12:50576426-50576445
11	CTCF	chr12:50576315-50576533	Medullo	brain:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
12	CTCF	chr12:50576099-50576784	A549	lung:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
13	CTCF	chr12:50576294-50576523	IMR90	lung:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
14	CTCF	chr12:50576260-50576410	HVMF	connective:	n/a	n/a
15	CTCF	chr12:50576271-50576611	K562	blood:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
16	CTCF	chr12:50576300-50576450	HPAF	blood vessel:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
17	CTCF	chr12:50576245-50576678	MCF-7	breast:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
18	RAD21	chr12:50576158-50576842	SK-N-SH	brain:	n/a	chr12:50576426-50576445
19	RAD21	chr12:50576123-50576814	HCT-116	colon:	n/a	chr12:50576426-50576445
20	STAT3	chr12:50576276-50576440	MCF10A-Er-Src	breast:	n/a	n/a
21	CTCF	chr12:50576280-50576430	HPF	lung:	n/a	n/a
22	CTCF	chr12:50576239-50576521	A549	lung:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
23	RAD21	chr12:50576194-50576723	A549	lung:	n/a	chr12:50576426-50576445
24	RAD21	chr12:50576262-50576452	K562	blood:	n/a	chr12:50576426-50576445
25	CTCF	chr12:50576280-50576430	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr12:50576190-50576632	A549	lung:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
27	CTCF	chr12:50576305-50576527	A549	lung:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
28	SMC3	chr12:50576316-50576537	K562	blood:	n/a	chr12:50576427-50576441
29	RAD21	chr12:50576133-50576761	A549	lung:	n/a	chr12:50576426-50576445
30	RAD21	chr12:50576292-50576589	HepG2	liver:	n/a	chr12:50576426-50576445
31	CTCF	chr12:50576220-50576370	HRPEpiC	eye:	n/a	n/a
32	CTCF	chr12:50576249-50576575	A549	lung:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
33	SMC3	chr12:50576307-50576573	HepG2	liver:	n/a	chr12:50576427-50576441
34	RAD21	chr12:50576277-50576591	A549	lung:	n/a	chr12:50576426-50576445
35	RAD21	chr12:50576177-50576669	HepG2	liver:	n/a	chr12:50576426-50576445

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50575985..50576844-chr12:50708187..50709140,4	K562	blood:

Variant related genes	Relation type
LIMA1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1044370	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169294	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169300	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11831413	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12426261	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12815871	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12824125	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12830386	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2178173	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2358538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34573394	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35549836	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35998534	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4883481	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883482	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56709084	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs646782	1.00[CHB][hapmap]
rs6580729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66768395	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs706793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136570	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7279	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7294548	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7297421	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7301566	0.98[ASN][1000 genomes]
rs7301649	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7302981	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7308356	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7532	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs836172	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs836177	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs836179	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs836180	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs860698	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1862043	CERS5	cis	Nerve Tibial	GTEx
rs1862043	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50561800-50582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:50561800-50582600	Weak transcription	Stomach Mucosa	stomach
3	chr12:50562000-50576400	Weak transcription	A549	lung
4	chr12:50562000-50584800	Weak transcription	K562	blood
5	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:50564400-50586200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:50567800-50578800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:50568200-50578200	Strong transcription	Fetal Intestine Large	intestine
10	chr12:50568600-50577800	Strong transcription	NHDF-Ad	bronchial
11	chr12:50568600-50582000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:50568800-50581400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr12:50569200-50577000	Strong transcription	Osteobl	bone
14	chr12:50569200-50579000	Strong transcription	NHEK	skin
15	chr12:50569400-50577800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:50569400-50579000	Weak transcription	Fetal Brain Male	brain
17	chr12:50569400-50581400	Weak transcription	Brain Substantia Nigra	brain
18	chr12:50569600-50579400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr12:50569800-50576400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:50569800-50577000	Strong transcription	Adipose Nuclei	Adipose
21	chr12:50569800-50577400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:50569800-50577800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:50569800-50578200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:50569800-50578200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:50569800-50578800	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:50570000-50577400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:50570000-50578000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:50570400-50592800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:50570600-50582800	Weak transcription	Small Intestine	intestine
31	chr12:50570800-50579800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:50570800-50580000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:50570800-50589800	Strong transcription	Fetal Stomach	stomach
34	chr12:50571200-50579000	Strong transcription	Fetal Intestine Small	intestine
35	chr12:50571600-50581400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:50571800-50579000	Weak transcription	Aorta	Aorta
37	chr12:50571800-50579000	Weak transcription	Pancreas	Pancrea
38	chr12:50571800-50579200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:50571800-50579800	Weak transcription	Gastric	stomach
40	chr12:50571800-50579800	Weak transcription	Psoas Muscle	Psoas
41	chr12:50571800-50580200	Weak transcription	HepG2	liver
42	chr12:50571800-50581400	Weak transcription	Spleen	Spleen
43	chr12:50571800-50586000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:50571800-50586200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
47	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:50572000-50579200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr12:50572000-50581600	Weak transcription	Colon Smooth Muscle	Colon

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