Variant report

Variant	rs4766899
Chromosome Location	chr12:118812693-118812694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr12:118812630-118813212	K562	blood:	n/a	n/a
2	POLR2A	chr12:118812671-118813098	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr12:118812323-118814598	K562	blood:	n/a	chr12:118813524-118813534 chr12:118813526-118813535

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:118666340..118669274-chr12:118811225..118812911,2	MCF-7	breast:
2	chr12:118670146..118671959-chr12:118810899..118813142,2	MCF-7	breast:
3	chr12:118577698..118580180-chr12:118811113..118813216,2	MCF-7	breast:
4	chr12:118674302..118676883-chr12:118810896..118813058,3	MCF-7	breast:
5	chr12:118789693..118801109-chr12:118805205..118813455,21	K562	blood:
6	chr12:118558717..118560861-chr12:118811542..118813614,2	K562	blood:
7	chr12:118601731..118605413-chr12:118811549..118815749,6	MCF-7	breast:
8	chr12:118573102..118576254-chr12:118808901..118815960,7	MCF-7	breast:
9	chr12:118812486..118814761-chr12:120105257..120106996,2	K562	blood:
10	chr12:118619933..118620906-chr12:118812675..118813644,2	K562	blood:
11	chr12:118604051..118606436-chr12:118810994..118813151,2	MCF-7	breast:
12	chr12:118791019..118798938-chr12:118809011..118813946,9	MCF-7	breast:
13	chr12:118792933..118800473-chr12:118805927..118813309,24	K562	blood:
14	chr12:118612128..118614340-chr12:118811467..118813100,2	MCF-7	breast:
15	chr12:118638724..118640594-chr12:118810784..118812979,2	K562	blood:

No data

Variant related genes	Relation type
SUDS3	TF binding region
TAOK3	TF binding region
ENSG00000221280	Chromatin interaction
ENSG00000089220	Chromatin interaction
ENSG00000248636	Chromatin interaction
ENSG00000176834	Chromatin interaction
ENSG00000111725	Chromatin interaction
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10082823	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10507286	0.85[CEU][hapmap]
rs1060964	1.00[CEU][hapmap]
rs10850967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850968	0.80[LWK][hapmap]
rs11068891	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs11068905	0.89[JPT][hapmap]
rs11068908	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs11068910	0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11068917	0.93[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs11068919	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11068926	0.94[EUR][1000 genomes]
rs12229607	0.93[CEU][hapmap]
rs12308475	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16948193	0.92[CEU][hapmap]
rs16948197	0.93[CEU][hapmap]
rs16948204	0.93[CEU][hapmap]
rs16948230	0.86[CEU][hapmap]
rs16948234	0.93[CEU][hapmap]
rs16948250	1.00[CEU][hapmap]
rs17440364	0.85[CEU][hapmap]
rs17440433	0.85[CEU][hapmap]
rs17440669	1.00[CEU][hapmap]
rs17440774	1.00[CEU][hapmap]
rs17440823	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17440893	1.00[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs17440942	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs17440956	1.00[CEU][hapmap]
rs17441033	0.92[CEU][hapmap]
rs17441061	1.00[CEU][hapmap]
rs17441075	0.92[CEU][hapmap]
rs17512142	0.85[CEU][hapmap]
rs17512177	0.83[CEU][hapmap]
rs17512198	0.85[CEU][hapmap]
rs17512219	0.85[CEU][hapmap]
rs17512407	0.93[CEU][hapmap]
rs17512483	1.00[CEU][hapmap]
rs17512525	1.00[CEU][hapmap]
rs17512574	0.93[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs17512609	0.93[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs17512644	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs17512652	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17512763	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs17619932	0.93[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs1909617	0.86[EUR][1000 genomes]
rs2036314	0.95[EUR][1000 genomes]
rs2036489	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055534	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2062519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280711	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs2784	1.00[CEU][hapmap]
rs4442583	0.94[EUR][1000 genomes]
rs4766900	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs4767669	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs4767670	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4767671	1.00[CEU][hapmap]
rs4767672	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs56133316	0.86[EUR][1000 genomes]
rs56157623	0.86[EUR][1000 genomes]
rs56284927	0.81[EUR][1000 genomes]
rs56324376	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59594854	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943365	0.82[EUR][1000 genomes]
rs61943367	0.86[EUR][1000 genomes]
rs61943368	0.86[EUR][1000 genomes]
rs61943369	0.95[EUR][1000 genomes]
rs61943370	0.94[EUR][1000 genomes]
rs61943371	0.94[EUR][1000 genomes]
rs61943385	0.86[EUR][1000 genomes]
rs61943388	0.86[EUR][1000 genomes]
rs61943389	0.86[EUR][1000 genomes]
rs61943391	0.85[EUR][1000 genomes]
rs61943392	0.86[EUR][1000 genomes]
rs61943393	0.86[EUR][1000 genomes]
rs61943397	0.87[EUR][1000 genomes]
rs61943399	0.86[EUR][1000 genomes]
rs61943400	0.86[EUR][1000 genomes]
rs61943401	0.86[EUR][1000 genomes]
rs61943402	0.86[EUR][1000 genomes]
rs61943403	0.87[EUR][1000 genomes]
rs61943404	0.86[EUR][1000 genomes]
rs61946063	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490173	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6490175	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490177	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7136676	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs7137055	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7137184	0.86[EUR][1000 genomes]
rs7294498	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295288	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7296214	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7299040	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs7302387	0.92[CEU][hapmap]
rs7303417	0.92[CEU][hapmap]
rs7304342	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7305647	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs7307393	1.00[CEU][hapmap]
rs7309484	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs7309671	1.00[CEU][hapmap]
rs7312555	1.00[CEU][hapmap]
rs7314987	0.93[CEU][hapmap]
rs7315458	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73205551	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73205576	0.86[EUR][1000 genomes]
rs73205594	0.86[EUR][1000 genomes]
rs7957828	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7961312	0.93[CEU][hapmap]
rs7962185	0.93[CEU][hapmap]
rs7965350	0.93[CEU][hapmap]
rs7967900	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7968011	0.86[EUR][1000 genomes]
rs7968371	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs884844	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs950288	0.86[EUR][1000 genomes]
rs965524	1.00[CEU][hapmap]
rs9943819	0.89[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4766899	SUDS3	cis	parietal	SCAN
rs4766899	SUDS3	Cis_1M	lymphoblastoid	RTeQTL
rs4766899	SUDS3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118811200-118813800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:118811200-118813800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:118811200-118813800	Weak transcription	Gastric	stomach
4	chr12:118811200-118813800	Weak transcription	Pancreas	Pancrea
5	chr12:118811400-118812800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:118811400-118813600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:118811400-118813800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:118811400-118813800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:118811400-118813800	Weak transcription	Aorta	Aorta
10	chr12:118811400-118813800	Weak transcription	Esophagus	oesophagus
11	chr12:118811400-118813800	Weak transcription	Lung	lung
12	chr12:118811600-118813200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:118811600-118813200	Enhancers	Brain Angular Gyrus	brain
14	chr12:118811600-118813600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:118811600-118813600	Weak transcription	Placenta	Placenta
16	chr12:118811600-118813800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:118811600-118813800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:118811600-118813800	Weak transcription	Ovary	ovary
19	chr12:118811800-118812800	Enhancers	Adipose Nuclei	Adipose
20	chr12:118811800-118812800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:118811800-118812800	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:118811800-118812800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:118811800-118812800	Enhancers	Osteobl	bone
24	chr12:118811800-118813000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:118811800-118813000	Enhancers	NHEK	skin
26	chr12:118811800-118813200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:118811800-118813200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:118811800-118813200	Weak transcription	Brain Anterior Caudate	brain
29	chr12:118811800-118813200	Enhancers	NHLF	lung
30	chr12:118811800-118813400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:118811800-118813400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:118811800-118813400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:118811800-118813400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:118811800-118813400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr12:118811800-118813400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:118811800-118813400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:118811800-118813400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:118811800-118813400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:118811800-118813400	Weak transcription	Brain Germinal Matrix	brain
40	chr12:118811800-118813400	Enhancers	Fetal Heart	heart
41	chr12:118811800-118813400	Weak transcription	Fetal Lung	lung
42	chr12:118811800-118813400	Weak transcription	Fetal Stomach	stomach
43	chr12:118811800-118813400	Weak transcription	Fetal Thymus	thymus
44	chr12:118811800-118813400	Weak transcription	NH-A	brain
45	chr12:118811800-118813600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:118811800-118813600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:118811800-118813600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:118811800-118813600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:118811800-118813600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:118811800-118813600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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