Variant report

Variant	rs10783342
Chromosome Location	chr12:50628466-50628467
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	ATF3	chr12:50628142-50628481	K562	blood:	n/a	n/a
2	USF1	chr12:50628190-50628497	K562	blood:	n/a	n/a
3	MXI1	chr12:50628263-50628499	Hela-S3	cervix:	n/a	chr12:50628351-50628360
4	FOS	chr12:50628164-50628506	MCF10A-Er-Src	breast:	n/a	chr12:50628324-50628335 chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
5	RAD21	chr12:50628128-50628638	HCT-116	colon:	n/a	n/a
6	MAX	chr12:50628195-50628605	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr12:50628202-50628650	MCF-7	breast:	n/a	n/a
8	MYC	chr12:50628152-50628536	Hela-S3	cervix:	n/a	n/a
9	MAX	chr12:50628217-50628596	SK-N-SH	brain:	n/a	n/a
10	MYC	chr12:50628138-50628607	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr12:50628320-50628470	GM12878	blood:	n/a	n/a
12	RAD21	chr12:50628135-50628485	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr12:50628157-50628689	HCT-116	colon:	n/a	n/a
14	RFX5	chr12:50628224-50628474	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr12:50628340-50628490	SAEC	small airway:	n/a	n/a
16	MAX	chr12:50628211-50628523	SK-N-SH	brain:	n/a	n/a
17	MYC	chr12:50628245-50628497	K562	blood:	n/a	n/a
18	MXI1	chr12:50628115-50628628	IMR90	lung:	n/a	chr12:50628351-50628360
19	RAD21	chr12:50628153-50628529	Hela-S3	cervix:	n/a	n/a
20	JUND	chr12:50628149-50628504	K562	blood:	n/a	chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334 chr12:50628324-50628335
21	MYC	chr12:50628170-50628573	MCF10A-Er-Src	breast:	n/a	n/a
22	RAD21	chr12:50628199-50628613	ECC-1	luminal epithelium:	n/a	n/a
23	FOSL1	chr12:50628052-50628634	HCT-116	colon:	n/a	chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628335 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
24	MAX	chr12:50628200-50628557	ECC-1	luminal epithelium:	n/a	n/a
25	USF2	chr12:50628168-50628530	Hela-S3	cervix:	n/a	n/a
26	MYC	chr12:50628128-50628646	A549	lung:	n/a	n/a
27	JUN	chr12:50628062-50628725	K562	blood:	n/a	chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
28	RAD21	chr12:50628099-50628531	MCF-7	breast:	n/a	n/a
29	FOS	chr12:50628191-50628491	HUVEC	blood vessel:	n/a	chr12:50628324-50628335 chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
30	USF1	chr12:50628211-50628583	ECC-1	luminal epithelium:	n/a	n/a
31	CBX3	chr12:50628125-50628497	K562	blood:	n/a	n/a
32	STAT3	chr12:50628242-50628487	MCF10A-Er-Src	breast:	n/a	chr12:50628405-50628417
33	JUND	chr12:50628169-50628514	Hela-S3	cervix:	n/a	chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334 chr12:50628324-50628335
34	USF1	chr12:50628242-50628533	ECC-1	luminal epithelium:	n/a	n/a
35	FOS	chr12:50628163-50628506	MCF10A-Er-Src	breast:	n/a	chr12:50628324-50628335 chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
36	JUND	chr12:50628051-50628672	SK-N-SH	brain:	n/a	chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334 chr12:50628324-50628335
37	RAD21	chr12:50628193-50628566	MCF-7	breast:	n/a	n/a
38	RXRA	chr12:50628199-50628545	SK-N-SH	brain:	n/a	n/a
39	CTCF	chr12:50628380-50628530	MCF-7	breast:	n/a	n/a
40	MAX	chr12:50628177-50628515	Hela-S3	cervix:	n/a	n/a
41	FOSL2	chr12:50628103-50628626	SK-N-SH	brain:	n/a	chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
42	USF1	chr12:50628107-50628618	HCT-116	colon:	n/a	n/a
43	FOSL2	chr12:50628127-50628596	A549	lung:	n/a	chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
44	RAD21	chr12:50628199-50628478	SK-N-SH_RA	brain:	n/a	n/a
45	FOSL1	chr12:50628076-50628485	K562	blood:	n/a	chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628335 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
46	MAX	chr12:50628179-50628506	K562	blood:	n/a	n/a
47	FOS	chr12:50628170-50628520	MCF10A-Er-Src	breast:	n/a	chr12:50628324-50628335 chr12:50628322-50628333 chr12:50628326-50628334 chr12:50628324-50628336 chr12:50628324-50628335 chr12:50628326-50628334 chr12:50628327-50628334
48	MAX	chr12:50628159-50628558	Hela-S3	cervix:	n/a	n/a
49	BACH1	chr12:50628310-50628468	H1-hESC	embryonic stem cell:	n/a	n/a
50	CBX3	chr12:50628059-50628712	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50628147..50630548-chr12:50634316..50636856,2	MCF-7	breast:

Variant related genes	Relation type
MIR1293	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10219559	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1044370	0.90[ASW][hapmap];0.93[LWK][hapmap];0.83[YRI][hapmap]
rs10747573	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10783343	0.88[AMR][1000 genomes]
rs1362984	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1862042	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2004283	0.93[AMR][1000 genomes]
rs2160994	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs2358538	0.89[ASW][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap]
rs4459386	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580729	0.90[ASW][hapmap];0.93[LWK][hapmap];0.91[YRI][hapmap]
rs6580732	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580734	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580738	0.88[LWK][hapmap];0.81[MKK][hapmap]
rs7136648	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301566	0.86[EUR][1000 genomes]
rs7308356	0.91[YRI][hapmap]
rs7308692	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309519	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957659	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8181679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668955	0.91[AMR][1000 genomes];0.83[EUR][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	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
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10783342	KIAA1463	cis	multi-tissue	Pritchard
rs10783342	CERS5	cis	Nerve Tibial	GTEx
rs10783342	SMARCD1	cis	cerebellum	SCAN
rs10783342	LASS5	cis	parietal	SCAN
rs10783342	DIP2B	cis	cerebellum	SCAN
rs10783342	EPLIN	cis	multi-tissue	Pritchard
rs10783342	MCRS1	cis	parietal	SCAN
rs10783342	LASS5	cis	cerebellum	SCAN
rs10783342	LASS5	cis	multi-tissue	Pritchard
rs10783342	NELL2	cis	cerebellum	SCAN
rs10783342	SLC4A8	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50599800-50635800	Weak transcription	Pancreas	Pancrea
2	chr12:50609200-50633200	Weak transcription	Small Intestine	intestine
3	chr12:50616200-50633200	Weak transcription	Lung	lung
4	chr12:50616400-50632000	Weak transcription	Fetal Brain Male	brain
5	chr12:50616400-50634000	Weak transcription	Gastric	stomach
6	chr12:50616400-50634000	Weak transcription	Ovary	ovary
7	chr12:50616400-50636200	Weak transcription	Left Ventricle	heart
8	chr12:50616600-50632200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:50616600-50634000	Weak transcription	Colonic Mucosa	Colon
10	chr12:50616600-50634000	Weak transcription	Psoas Muscle	Psoas
11	chr12:50616600-50634000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:50616800-50636400	Weak transcription	Aorta	Aorta
13	chr12:50616800-50641600	Weak transcription	Brain Angular Gyrus	brain
14	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
15	chr12:50617000-50632800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:50617000-50634000	Weak transcription	NHLF	lung
17	chr12:50617000-50636200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:50617200-50633000	Strong transcription	Fetal Intestine Small	intestine
19	chr12:50617400-50634600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:50617400-50635600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:50617600-50638400	Weak transcription	Brain Germinal Matrix	brain
22	chr12:50618600-50633800	Weak transcription	NHDF-Ad	bronchial
23	chr12:50618600-50634000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:50618600-50634000	Weak transcription	Osteobl	bone
25	chr12:50618600-50634400	Weak transcription	HSMM	muscle
26	chr12:50618600-50636200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:50618600-50638400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:50618600-50640000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:50623000-50638400	Weak transcription	Fetal Brain Female	brain
30	chr12:50625400-50634000	Weak transcription	HSMMtube	muscle
31	chr12:50625400-50634400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:50626600-50628800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:50626600-50628800	Enhancers	NHEK	skin
34	chr12:50626800-50629000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:50626800-50633200	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:50627000-50628800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:50627200-50629000	Enhancers	Hela-S3	cervix
38	chr12:50627200-50632800	Weak transcription	Adipose Nuclei	Adipose
39	chr12:50627200-50635200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:50627400-50634000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:50627600-50634400	Weak transcription	Fetal Lung	lung
42	chr12:50627600-50644600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:50628000-50628600	Enhancers	K562	blood
44	chr12:50628000-50628800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:50628000-50628800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:50628000-50628800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:50628000-50628800	Enhancers	Placenta	Placenta
48	chr12:50628000-50628800	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr12:50628200-50628600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr12:50628200-50628600	Enhancers	Skeletal Muscle Female	skeletal muscle

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