Variant report

Variant	rs11834369
Chromosome Location	chr12:124059546-124059547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124056996..124059825-chr12:124068978..124071238,2	MCF-7	breast:
2	chr12:124056030..124058750-chr12:124059393..124062222,4	K562	blood:
3	chr12:124056886..124060484-chr12:124067247..124069927,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086598	Chromatin interaction
ENSG00000247373	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11057298	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057302	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057306	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610013	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615043	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11829661	0.81[AFR][1000 genomes]
rs11837236	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099981	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099985	0.83[AFR][1000 genomes]
rs12099986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877365	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340691	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3209852	0.81[ASN][1000 genomes]
rs34099549	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850953	0.81[AFR][1000 genomes]
rs4930715	0.96[EUR][1000 genomes]
rs61678733	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488881	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6488882	0.81[AFR][1000 genomes]
rs7136101	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7301377	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303554	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316613	0.94[EUR][1000 genomes]
rs73414262	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786428	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786429	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786431	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786432	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786433	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786434	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786435	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786437	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786438	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786439	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786450	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786455	0.80[EUR][1000 genomes]
rs7954782	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7958153	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960812	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964934	0.82[AFR][1000 genomes]
rs7965292	0.83[AFR][1000 genomes]
rs7965466	0.84[EUR][1000 genomes]
rs7968040	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970545	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971779	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973187	0.81[AFR][1000 genomes]
rs7973689	0.81[AFR][1000 genomes]
rs952360	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11834369	DDX55	cis	Thyroid	GTEx
rs11834369	RP11-486O12.2	cis	Artery Aorta	GTEx
rs11834369	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs11834369	RP11-486O12.2	cis	Esophagus Muscularis	GTEx
rs11834369	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs11834369	RP11-486O12.2	cis	Nerve Tibial	GTEx
rs11834369	RP11-486O12.2	cis	Stomach	GTEx
rs11834369	RP11-486O12.2	cis	Heart Left Ventricle	GTEx
rs11834369	DDX55	cis	lung	GTEx
rs11834369	RP11-486O12.2	cis	Thyroid	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124055000-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:124055000-124067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:124055200-124060800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:124055200-124068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:124055400-124067800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:124055800-124060400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:124055800-124060600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:124056000-124060800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:124056000-124066600	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:124056000-124066600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:124056000-124067000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:124056000-124067800	Weak transcription	Lung	lung
13	chr12:124056200-124060600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:124056200-124064800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:124056200-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:124056200-124066600	Weak transcription	Thymus	Thymus
17	chr12:124056200-124067000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:124056200-124067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:124056400-124060400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:124056400-124060400	Weak transcription	A549	lung
21	chr12:124056400-124060600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:124056400-124065200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:124056400-124065400	Weak transcription	Osteobl	bone
24	chr12:124056400-124066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:124056400-124066600	Weak transcription	Adipose Nuclei	Adipose
26	chr12:124056400-124066600	Weak transcription	Brain Anterior Caudate	brain
27	chr12:124056400-124066600	Weak transcription	K562	blood
28	chr12:124056400-124066800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:124056400-124066800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:124056400-124067000	Weak transcription	NHDF-Ad	bronchial
31	chr12:124056400-124067400	Weak transcription	HSMMtube	muscle
32	chr12:124056800-124066600	Weak transcription	Dnd41	blood
33	chr12:124058800-124066600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:124058800-124067000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:124059200-124060200	Weak transcription	Fetal Lung	lung
36	chr12:124059200-124066800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:124059200-124066800	Weak transcription	Spleen	Spleen
38	chr12:124059200-124067200	Weak transcription	Brain Germinal Matrix	brain
39	chr12:124059400-124060600	Weak transcription	Fetal Intestine Large	intestine
40	chr12:124059400-124066600	Weak transcription	Liver	Liver
41	chr12:124059400-124067000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:124059400-124067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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