Variant report

Variant	rs56324376
Chromosome Location	chr12:118809939-118809940
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	ELF1	chr12:118809210-118810081	GM12878	blood:	n/a	n/a
2	ZNF263	chr12:118808712-118810011	HEK293-T-REx	kidney:	n/a	chr12:118809600-118809609
3	ZBTB7A	chr12:118809301-118810941	ECC-1	luminal epithelium:	n/a	chr12:118809551-118809559 chr12:118809487-118809501 chr12:118809571-118809579
4	SIN3A	chr12:118809151-118811330	H1-hESC	embryonic stem cell:	n/a	chr12:118810584-118810595 chr12:118810689-118810702 chr12:118809983-118809996 chr12:118809980-118809989
5	ZBTB7A	chr12:118809804-118810241	HepG2	liver:	n/a	n/a
6	ZBTB7A	chr12:118809116-118810104	K562	blood:	n/a	chr12:118809551-118809559 chr12:118809487-118809501 chr12:118809571-118809579
7	ZBTB7A	chr12:118809083-118811191	K562	blood:	n/a	chr12:118809551-118809559 chr12:118809487-118809501 chr12:118809571-118809579
8	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
ENSG00000135090	Chromatin interaction
ENSG00000176834	Chromatin interaction
ENSG00000089220	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

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]
rs10850967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068910	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11068917	0.88[EUR][1000 genomes]
rs11068919	0.91[EUR][1000 genomes]
rs11068926	0.94[EUR][1000 genomes]
rs12308475	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17440823	0.81[EUR][1000 genomes]
rs17440893	0.85[EUR][1000 genomes]
rs17440942	0.86[EUR][1000 genomes]
rs17512574	0.81[EUR][1000 genomes]
rs17512609	0.82[EUR][1000 genomes]
rs17512644	0.83[EUR][1000 genomes]
rs17512652	0.83[EUR][1000 genomes]
rs17512763	0.86[EUR][1000 genomes]
rs17619932	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	0.86[EUR][1000 genomes]
rs2062519	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4442583	0.94[EUR][1000 genomes]
rs4766899	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766900	0.87[EUR][1000 genomes]
rs4767669	0.86[EUR][1000 genomes]
rs4767670	0.86[EUR][1000 genomes]
rs4767672	0.86[EUR][1000 genomes]
rs56133316	0.86[EUR][1000 genomes]
rs56157623	0.86[EUR][1000 genomes]
rs56284927	0.81[EUR][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	0.80[EUR][1000 genomes]
rs6490175	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490177	0.93[EUR][1000 genomes]
rs7137055	0.86[EUR][1000 genomes]
rs7137184	0.86[EUR][1000 genomes]
rs7294498	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295288	0.80[EUR][1000 genomes]
rs7296214	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7299040	0.86[EUR][1000 genomes]
rs7304342	0.87[EUR][1000 genomes]
rs7309484	0.86[EUR][1000 genomes]
rs7315458	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73205551	0.84[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	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7967900	0.86[EUR][1000 genomes]
rs7968011	0.86[EUR][1000 genomes]
rs7968371	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs884844	0.86[EUR][1000 genomes]
rs950288	0.86[EUR][1000 genomes]
rs9943819	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56324376	SUDS3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118807200-118811400	Active TSS	NHDF-Ad	bronchial
2	chr12:118808000-118811400	Active TSS	NHLF	lung
3	chr12:118808200-118810000	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr12:118808400-118810000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:118808400-118811200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:118808400-118811200	Active TSS	Brain Anterior Caudate	brain
7	chr12:118808400-118811200	Active TSS	Duodenum Mucosa	Duodenum
8	chr12:118808400-118811200	Active TSS	Fetal Intestine Large	intestine
9	chr12:118808400-118811600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:118808600-118810000	Bivalent/Poised TSS	Fetal Kidney	kidney
11	chr12:118808600-118811400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:118808600-118811400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:118808600-118811400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:118808600-118811400	Active TSS	Brain Substantia Nigra	brain
15	chr12:118808600-118811400	Active TSS	Colonic Mucosa	Colon
16	chr12:118808600-118811600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:118808600-118811800	Active TSS	Right Atrium	heart
18	chr12:118808800-118810000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:118808800-118810000	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr12:118808800-118810200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:118808800-118810200	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr12:118808800-118810200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:118808800-118810400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr12:118808800-118810400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr12:118808800-118810600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:118808800-118811000	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr12:118808800-118811200	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr12:118808800-118811200	Active TSS	Fetal Intestine Small	intestine
29	chr12:118808800-118811200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr12:118808800-118811200	Active TSS	HMEC	breast
31	chr12:118808800-118811400	Active TSS	Rectal Smooth Muscle	rectum
32	chr12:118808800-118811400	Active TSS	Right Ventricle	heart
33	chr12:118808800-118811400	Active TSS	GM12878-XiMat	blood
34	chr12:118809000-118810000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr12:118809000-118810000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:118809000-118810000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:118809000-118810000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr12:118809000-118810000	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr12:118809000-118810000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr12:118809000-118810000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
41	chr12:118809000-118810000	Flanking Bivalent TSS/Enh	Dnd41	blood
42	chr12:118809000-118810200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr12:118809000-118810200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
44	chr12:118809000-118811000	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr12:118809000-118811200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:118809000-118811200	Active TSS	Brain Hippocampus Middle	brain
47	chr12:118809000-118811200	Active TSS	Gastric	stomach
48	chr12:118809000-118811200	Active TSS	Pancreas	Pancrea
49	chr12:118809000-118811200	Active TSS	HSMMtube	muscle
50	chr12:118809000-118811200	Active TSS	NH-A	brain

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