Variant report

Variant	rs1939110
Chromosome Location	chr11:86515072-86515073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86168596..86172615-chr11:86512849..86516301,3	MCF-7	breast:
2	chr11:86345451..86347957-chr11:86512981..86515684,2	MCF-7	breast:
3	chr11:86194046..86196274-chr11:86514380..86517149,2	MCF-7	breast:
4	chr11:86411235..86420303-chr11:86507153..86518645,29	MCF-7	breast:
5	chr11:86509457..86512204-chr11:86513556..86515682,3	K562	blood:
6	chr11:86166230..86170690-chr11:86512399..86515625,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254731	Chromatin interaction
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11234809	0.85[ASN][1000 genomes]
rs11601553	0.86[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs11602695	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12361769	0.84[ASN][1000 genomes]
rs12366016	0.84[ASN][1000 genomes]
rs12420039	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12421517	0.92[ASN][1000 genomes]
rs12421942	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12574979	0.86[ASN][1000 genomes]
rs12797648	0.82[ASN][1000 genomes]
rs12802848	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs12809023	0.85[ASN][1000 genomes]
rs17211926	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs17212012	0.86[ASN][1000 genomes]
rs17819068	0.86[JPT][hapmap]
rs17819134	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17819181	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs17819187	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1807014	0.83[ASN][1000 genomes]
rs1939111	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1939112	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1939113	0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1939114	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1939115	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1939116	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1939117	0.85[ASN][1000 genomes]
rs1954769	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2155080	0.89[ASN][1000 genomes]
rs2155081	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs28517777	0.83[ASN][1000 genomes]
rs35902217	0.85[ASN][1000 genomes]
rs36061072	0.85[ASN][1000 genomes]
rs3809048	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4128368	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4269941	0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4291699	0.87[ASN][1000 genomes]
rs4304806	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4307743	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4307748	0.87[ASN][1000 genomes]
rs4423210	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4485132	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4495915	0.83[ASN][1000 genomes]
rs4570601	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4944630	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs55646317	0.84[ASN][1000 genomes]
rs58976693	0.84[ASN][1000 genomes]
rs61707378	0.83[ASN][1000 genomes]
rs6592315	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7105467	0.82[ASN][1000 genomes]
rs7108490	0.87[ASN][1000 genomes]
rs7118751	0.85[ASN][1000 genomes]
rs7120185	0.85[ASN][1000 genomes]
rs7123349	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7126492	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7131625	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs744292	0.84[ASN][1000 genomes]
rs7931274	0.85[ASN][1000 genomes]
rs7940201	0.82[ASN][1000 genomes]
rs7948063	0.82[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs7951582	0.82[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv521505	chr11:86438115-86515072	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2756074	chr11:86456552-86729552	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv523704	chr11:86508928-86528437	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv2760199	chr11:86512312-86531118	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1939110	TYR	cis	cerebellum	SCAN
rs1939110	CCDC89	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86512000-86527000	Weak transcription	Spleen	Spleen
2	chr11:86512400-86515600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:86512400-86515800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:86512600-86515400	Flanking Active TSS	HUVEC	blood vessel
5	chr11:86512600-86518600	Weak transcription	Small Intestine	intestine
6	chr11:86512600-86520600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:86512800-86516000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr11:86512800-86516200	Weak transcription	Fetal Heart	heart
9	chr11:86512800-86516800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:86512800-86517400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:86512800-86518400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:86512800-86522800	Weak transcription	Pancreas	Pancrea
13	chr11:86513200-86519200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:86513400-86515800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:86513400-86517200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:86513400-86520400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:86513600-86515600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:86513600-86515800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:86513600-86517600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:86513600-86518600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:86513600-86518600	Weak transcription	Lung	lung
22	chr11:86513600-86525600	Weak transcription	Colonic Mucosa	Colon
23	chr11:86513800-86515200	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr11:86513800-86515600	Weak transcription	HSMMtube	muscle
25	chr11:86513800-86515800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:86513800-86516200	Weak transcription	Adipose Nuclei	Adipose
27	chr11:86513800-86522200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:86513800-86522600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:86514000-86516000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr11:86514000-86516000	Weak transcription	Ovary	ovary
31	chr11:86514000-86516000	Weak transcription	Right Atrium	heart
32	chr11:86514000-86516200	Weak transcription	Fetal Stomach	stomach
33	chr11:86514000-86516400	Weak transcription	Stomach Mucosa	stomach
34	chr11:86514000-86516600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:86514000-86517200	Enhancers	NHLF	lung
36	chr11:86514000-86518200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:86514000-86518600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:86514000-86523200	Weak transcription	Psoas Muscle	Psoas
39	chr11:86514000-86525400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:86514000-86530000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr11:86514200-86515200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr11:86514200-86515200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr11:86514200-86516000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr11:86514200-86517600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:86514200-86520400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr11:86514200-86525600	Weak transcription	Fetal Lung	lung
47	chr11:86514400-86515400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:86514400-86515400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr11:86514400-86516800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:86514400-86517200	Transcr. at gene 5' and 3'	A549	lung

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