Variant report

Variant	rs786433
Chromosome Location	chr12:124089582-124089583
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124084988..124092992-chr12:124114351..124121638,14	K562	blood:
2	chr12:124085831..124093816-chr12:124094373..124101211,18	MCF-7	breast:
3	chr12:124088481..124090749-chr12:124100690..124102961,3	K562	blood:

Variant related genes	Relation type
ENSG00000111364	Chromatin interaction
ENSG00000206897	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000111358	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11057298	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057302	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057306	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610013	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834369	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837236	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099981	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099986	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877365	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340691	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3209852	0.81[ASN][1000 genomes]
rs34099549	1.00[ASN][1000 genomes]
rs4930715	0.94[EUR][1000 genomes]
rs61678733	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488881	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7136101	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7301377	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303554	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316613	0.91[EUR][1000 genomes]
rs73414262	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786428	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786429	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786431	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786432	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786434	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786435	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786437	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786438	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786439	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786450	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954782	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7958153	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960812	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965466	0.82[EUR][1000 genomes]
rs7968040	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970545	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971779	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952360	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs786433	DDX55	cis	lung	GTEx
rs786433	RP11-486O12.2	cis	Heart Left Ventricle	GTEx
rs786433	RP11-486O12.2	cis	Nerve Tibial	GTEx
rs786433	RP11-486O12.2	cis	Thyroid	GTEx
rs786433	DDX55	cis	Thyroid	GTEx
rs786433	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs786433	RP11-486O12.2	cis	Esophagus Muscularis	GTEx
rs786433	DDX55	cis	Esophagus Muscularis	GTEx
rs786433	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs786433	RP11-486O12.2	cis	Adipose Subcutaneous	GTEx
rs786433	RP11-486O12.2	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124087600-124091800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:124087800-124089600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:124087800-124089600	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:124087800-124089600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:124087800-124089800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:124087800-124090000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:124087800-124090200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:124087800-124090200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:124087800-124090200	Weak transcription	Esophagus	oesophagus
10	chr12:124087800-124090200	Weak transcription	Right Ventricle	heart
11	chr12:124087800-124090400	Weak transcription	Fetal Kidney	kidney
12	chr12:124087800-124090600	Weak transcription	Psoas Muscle	Psoas
13	chr12:124087800-124091200	Weak transcription	Colonic Mucosa	Colon
14	chr12:124087800-124091200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:124087800-124091400	Weak transcription	Aorta	Aorta
16	chr12:124087800-124091400	Weak transcription	Brain Substantia Nigra	brain
17	chr12:124087800-124092000	Weak transcription	Small Intestine	intestine
18	chr12:124087800-124102000	Weak transcription	Stomach Mucosa	stomach
19	chr12:124087800-124109600	Weak transcription	Right Atrium	heart
20	chr12:124088000-124089600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:124088000-124089600	Weak transcription	NHLF	lung
22	chr12:124088000-124089800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:124088000-124089800	Weak transcription	NHDF-Ad	bronchial
24	chr12:124088000-124089800	Weak transcription	Osteobl	bone
25	chr12:124088000-124090000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:124088000-124090000	Weak transcription	HMEC	breast
27	chr12:124088000-124090200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:124088000-124090200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:124088000-124090200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:124088000-124090200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:124088000-124090200	Weak transcription	Adipose Nuclei	Adipose
32	chr12:124088000-124090200	Weak transcription	Fetal Brain Female	brain
33	chr12:124088000-124090200	Weak transcription	Gastric	stomach
34	chr12:124088000-124090200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:124088000-124090200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:124088000-124090200	Weak transcription	HSMM	muscle
37	chr12:124088000-124090600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr12:124088000-124090600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:124088000-124099200	Weak transcription	Fetal Heart	heart
40	chr12:124088000-124107200	Strong transcription	K562	blood
41	chr12:124088200-124089600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:124088200-124089800	Weak transcription	Thymus	Thymus
43	chr12:124088200-124090200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:124088200-124090200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:124088200-124098800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:124088200-124116000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:124088200-124117000	Strong transcription	Fetal Stomach	stomach
48	chr12:124088400-124089800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:124088400-124089800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:124088400-124089800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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