Variant report

Variant	rs514826
Chromosome Location	chr12:118809303-118809304
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	EBF1	chr12:118809251-118809602	GM12878	blood:	n/a	n/a
2	MXI1	chr12:118809282-118809448	GM12878	blood:	n/a	n/a
3	MAZ	chr12:118809089-118809728	K562	blood:	n/a	chr12:118809523-118809533 chr12:118809529-118809539
4	POLR2A	chr12:118809255-118809582	Gliobla	brain:	n/a	n/a
5	UBTF	chr12:118809004-118809619	K562	blood:	n/a	n/a
6	ELF1	chr12:118809210-118810081	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:118809194-118809755	K562	blood:	n/a	n/a
8	CCNT2	chr12:118809119-118809894	K562	blood:	n/a	n/a
9	MAX	chr12:118809180-118809626	GM12878	blood:	n/a	chr12:118809523-118809533 chr12:118809529-118809539
10	ZNF263	chr12:118808712-118810011	HEK293-T-REx	kidney:	n/a	chr12:118809600-118809609
11	TBP	chr12:118809131-118809324	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr12:118809119-118809319	MCF10A-Er-Src	breast:	n/a	n/a
13	MAX	chr12:118809085-118809598	K562	blood:	n/a	chr12:118809523-118809533 chr12:118809529-118809539
14	HMGN3	chr12:118809232-118809743	K562	blood:	n/a	n/a
15	ZBTB7A	chr12:118809301-118810941	ECC-1	luminal epithelium:	n/a	chr12:118809551-118809559 chr12:118809487-118809501 chr12:118809571-118809579
16	SIN3A	chr12:118809151-118811330	H1-hESC	embryonic stem cell:	n/a	chr12:118810584-118810595 chr12:118810689-118810702 chr12:118809983-118809996 chr12:118809980-118809989
17	POLR2A	chr12:118809258-118809326	ProgFib	skin:	n/a	n/a
18	MYC	chr12:118809216-118809351	K562	blood:	n/a	n/a
19	GATA3	chr12:118808477-118809580	MCF-7	breast:	n/a	n/a
20	GATA3	chr12:118808468-118809386	MCF-7	breast:	n/a	n/a
21	RAD21	chr12:118809291-118809369	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr12:118808537-118809851	IMR90	lung:	n/a	n/a
23	NR2F2	chr12:118808613-118809573	MCF-7	breast:	n/a	chr12:118809107-118809122
24	CTCF	chr12:118809260-118809410	HCPEpiC	choroid plexus:	n/a	n/a
25	RAD21	chr12:118809070-118809519	SK-N-SH_RA	brain:	n/a	n/a
26	ZBTB7A	chr12:118809116-118810104	K562	blood:	n/a	chr12:118809551-118809559 chr12:118809487-118809501 chr12:118809571-118809579
27	GATA3	chr12:118809024-118809516	T-47D	breast:	n/a	n/a
28	ZNF143	chr12:118809130-118809841	GM12878	blood:	n/a	chr12:118809523-118809533
29	ZBTB7A	chr12:118809083-118811191	K562	blood:	n/a	chr12:118809551-118809559 chr12:118809487-118809501 chr12:118809571-118809579
30	UBTF	chr12:118809107-118809505	K562	blood:	n/a	n/a
31	ZBTB7A	chr12:118809253-118810938	ECC-1	luminal epithelium:	n/a	chr12:118809551-118809559 chr12:118809487-118809501 chr12:118809571-118809579

No.	Distal block	Cell Line	Cell type
1	chr12:118789693..118801109-chr12:118805205..118813455,21	K562	blood:
2	chr12:118573102..118576254-chr12:118808901..118815960,7	MCF-7	breast:
3	chr12:118765311..118767097-chr12:118807777..118809983,2	K562	blood:
4	chr12:118791019..118798938-chr12:118809011..118813946,9	MCF-7	breast:
5	chr12:118792933..118800473-chr12:118805927..118813309,24	K562	blood:

Variant related genes	Relation type
SUDS3	TF binding region
ENSG00000089220	Chromatin interaction
ENSG00000135090	Chromatin interaction
ENSG00000176834	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1699160	0.92[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs191626	0.82[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs2279833	0.81[ASN][1000 genomes]
rs353897	0.83[ASW][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap]
rs428073	0.92[ASW][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.87[YRI][hapmap]
rs431038	0.95[JPT][hapmap]
rs459547	0.81[ASN][1000 genomes]
rs464227	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs521048	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs556081	0.92[ASW][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs572869	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59848754	0.82[AFR][1000 genomes]
rs7307848	0.81[ASN][1000 genomes]
rs882926	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv899547	chr12:118791441-118896304	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv3413770	chr12:118808569-118812117	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs514826	SUDS3	cis	cerebellum	SCAN
rs514826	OAS2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118807200-118809400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:118807200-118811400	Active TSS	NHDF-Ad	bronchial
3	chr12:118808000-118809400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr12:118808000-118811400	Active TSS	NHLF	lung
5	chr12:118808200-118809600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:118808200-118810000	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr12:118808400-118809400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:118808400-118809400	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr12:118808400-118809600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr12:118808400-118810000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr12:118808400-118811200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:118808400-118811200	Active TSS	Brain Anterior Caudate	brain
13	chr12:118808400-118811200	Active TSS	Duodenum Mucosa	Duodenum
14	chr12:118808400-118811200	Active TSS	Fetal Intestine Large	intestine
15	chr12:118808400-118811600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:118808600-118809400	Flanking Active TSS	HUVEC	blood vessel
17	chr12:118808600-118809600	Bivalent/Poised TSS	Fetal Brain Female	brain
18	chr12:118808600-118810000	Bivalent/Poised TSS	Fetal Kidney	kidney
19	chr12:118808600-118811400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:118808600-118811400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:118808600-118811400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:118808600-118811400	Active TSS	Brain Substantia Nigra	brain
23	chr12:118808600-118811400	Active TSS	Colonic Mucosa	Colon
24	chr12:118808600-118811600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:118808600-118811800	Active TSS	Right Atrium	heart
26	chr12:118808800-118809400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:118808800-118809400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr12:118808800-118809600	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr12:118808800-118809600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:118808800-118809600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:118808800-118809800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr12:118808800-118809800	Bivalent Enhancer	Fetal Brain Male	brain
33	chr12:118808800-118810000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:118808800-118810000	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr12:118808800-118810200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
36	chr12:118808800-118810200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr12:118808800-118810200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:118808800-118810400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr12:118808800-118810400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr12:118808800-118810600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:118808800-118811000	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr12:118808800-118811200	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr12:118808800-118811200	Active TSS	Fetal Intestine Small	intestine
44	chr12:118808800-118811200	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr12:118808800-118811200	Active TSS	HMEC	breast
46	chr12:118808800-118811400	Active TSS	Rectal Smooth Muscle	rectum
47	chr12:118808800-118811400	Active TSS	Right Ventricle	heart
48	chr12:118808800-118811400	Active TSS	GM12878-XiMat	blood
49	chr12:118809000-118809400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:118809000-118809400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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