Variant report

Variant	rs11038339
Chromosome Location	chr11:45191857-45191858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45167650..45170338-chr11:45189685..45192446,3	MCF-7	breast:
2	chr11:45175178..45177497-chr11:45190478..45192901,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10444286	1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769123	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838439	0.82[JPT][hapmap]
rs11038341	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11038350	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs12292233	1.00[YRI][hapmap]
rs3886790	0.89[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55646648	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907072	0.86[AFR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11038339	PRDM11	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45180000-45193000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:45181600-45193600	Weak transcription	Fetal Intestine Large	intestine
3	chr11:45183600-45200400	Weak transcription	Esophagus	oesophagus
4	chr11:45183800-45201200	Weak transcription	Gastric	stomach
5	chr11:45186000-45193000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr11:45186400-45201200	Weak transcription	Brain Substantia Nigra	brain
7	chr11:45186600-45201400	Weak transcription	Fetal Brain Female	brain
8	chr11:45186800-45200600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:45188400-45193400	Weak transcription	Fetal Intestine Small	intestine
10	chr11:45189800-45192400	Enhancers	Ovary	ovary
11	chr11:45190000-45192200	Enhancers	Fetal Muscle Leg	muscle
12	chr11:45190000-45192200	Enhancers	Pancreas	Pancrea
13	chr11:45190200-45193400	Enhancers	Right Atrium	heart
14	chr11:45190400-45192200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:45190400-45192400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr11:45190400-45193400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:45190600-45192000	Weak transcription	Lung	lung
18	chr11:45190600-45192200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:45190600-45192200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:45190600-45198400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr11:45190800-45192200	Enhancers	HepG2	liver
22	chr11:45191000-45192400	Enhancers	Right Ventricle	heart
23	chr11:45191000-45192800	Enhancers	Left Ventricle	heart
24	chr11:45191200-45192600	Enhancers	Fetal Heart	heart
25	chr11:45191200-45199000	Weak transcription	Fetal Stomach	stomach
26	chr11:45191400-45192200	Weak transcription	Spleen	Spleen
27	chr11:45191400-45195600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:45191600-45198400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:45191800-45192200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:45191800-45198600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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