Variant report

Variant	rs3886790
Chromosome Location	chr11:45180555-45180556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45168840..45171324-chr11:45179427..45182574,4	K562	blood:
2	chr11:45179374..45181360-chr11:45184809..45187751,2	K562	blood:
3	chr11:45176255..45180138-chr11:45180420..45184771,5	MCF-7	breast:
4	chr11:45178718..45181474-chr11:45186088..45187942,2	K562	blood:
5	chr11:45166948..45170773-chr11:45176737..45181280,4	K562	blood:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10444286	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769123	0.89[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838428	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838439	0.82[JPT][hapmap]
rs11038339	0.89[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038341	0.89[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11038350	0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs55646648	0.94[AMR][1000 genomes];0.95[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	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv541025	chr11:45154352-45193352	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv523057	chr11:45174530-45181682	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3886790	PRDM11	cis	Thyroid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45169400-45181600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:45169800-45188000	Weak transcription	Primary T cells from cord blood	blood
3	chr11:45170000-45190000	Weak transcription	Primary B cells from cord blood	blood
4	chr11:45170400-45185200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:45170800-45180800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:45172400-45190000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:45175400-45182800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:45175600-45186200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:45176000-45181400	Enhancers	Right Ventricle	heart
10	chr11:45176000-45181400	Enhancers	Spleen	Spleen
11	chr11:45176000-45181600	Enhancers	Placenta	Placenta
12	chr11:45176000-45184200	Enhancers	Fetal Lung	lung
13	chr11:45176000-45186600	Genic enhancers	Fetal Stomach	stomach
14	chr11:45176200-45181800	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr11:45176600-45183600	Enhancers	Esophagus	oesophagus
16	chr11:45177800-45180800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:45178200-45181200	Enhancers	Ovary	ovary
18	chr11:45178200-45183600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:45178200-45187600	Enhancers	Fetal Heart	heart
20	chr11:45178400-45181000	Enhancers	Duodenum Mucosa	Duodenum
21	chr11:45178400-45181400	Enhancers	Right Atrium	heart
22	chr11:45178400-45181800	Enhancers	Left Ventricle	heart
23	chr11:45178400-45185200	Enhancers	Fetal Muscle Leg	muscle
24	chr11:45178600-45180600	Enhancers	Pancreas	Pancrea
25	chr11:45178600-45180600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr11:45178600-45181000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr11:45178600-45181200	Enhancers	Brain Anterior Caudate	brain
28	chr11:45178600-45181800	Enhancers	Lung	lung
29	chr11:45178800-45180800	Enhancers	Brain Substantia Nigra	brain
30	chr11:45178800-45181000	Enhancers	Brain Hippocampus Middle	brain
31	chr11:45178800-45181400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr11:45178800-45181600	Enhancers	Brain Angular Gyrus	brain
33	chr11:45178800-45184000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:45178800-45186800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr11:45179000-45180600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr11:45179000-45180600	Enhancers	Small Intestine	intestine
37	chr11:45179000-45180800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr11:45179000-45181200	Enhancers	Brain Cingulate Gyrus	brain
39	chr11:45179000-45181200	Enhancers	Brain Germinal Matrix	brain
40	chr11:45179000-45181200	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr11:45179000-45181400	Enhancers	Fetal Thymus	thymus
42	chr11:45179000-45181600	Enhancers	Fetal Intestine Large	intestine
43	chr11:45179000-45181800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr11:45179200-45180600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:45179200-45180800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:45179200-45180800	Enhancers	Colonic Mucosa	Colon
47	chr11:45179200-45180800	Enhancers	HSMMtube	muscle
48	chr11:45179200-45181000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:45179200-45181000	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr11:45179200-45181400	Enhancers	Adipose Nuclei	Adipose

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