Variant report

Variant	rs1892939
Chromosome Location	chr11:65986258-65986259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65985337..65987041-chr11:66126472..66128727,2	K562	blood:
2	chr11:65985101..65987489-chr11:65988422..65991212,2	MCF-7	breast:
3	chr11:65985362..65987723-chr11:66025146..66026929,2	MCF-7	breast:
4	chr11:65985243..65987105-chr11:65991157..65993460,2	K562	blood:

Variant related genes	Relation type
ENSG00000174996	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10791865	0.98[ASN][1000 genomes]
rs10896104	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1115508	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151537	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1151539	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1151540	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203798	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1717669	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508657	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3016319	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474005	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521109	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs524859	0.86[AFR][1000 genomes]
rs528842	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555360	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555853	0.94[ASN][1000 genomes]
rs556595	0.86[EUR][1000 genomes]
rs708471	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs708472	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs801731	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801734	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801735	0.89[EUR][1000 genomes]
rs801736	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801737	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801739	0.95[EUR][1000 genomes]
rs801741	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9326370	0.86[AMR][1000 genomes];0.98[EUR][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	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1892939	RP11-867G23.1	cis	Muscle Skeletal	GTEx
rs1892939	KLC2	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65958800-65989200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:65959200-65989400	Weak transcription	K562	blood
3	chr11:65961400-66011200	Weak transcription	Psoas Muscle	Psoas
4	chr11:65964000-65989600	Weak transcription	Stomach Mucosa	stomach
5	chr11:65976400-65989200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:65976400-65989600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr11:65976600-66006000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:65976800-65989600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:65976800-65996000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:65977000-65989800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:65977200-65996000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:65977400-65990000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:65977400-66010600	Strong transcription	Fetal Stomach	stomach
14	chr11:65977600-65989400	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr11:65977600-65989400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:65977600-65989600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr11:65977600-65989800	Strong transcription	Fetal Intestine Small	intestine
18	chr11:65977600-66018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:65977800-65987800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:65977800-65987800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:65977800-65988800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:65977800-65988800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:65977800-65988800	Strong transcription	Lung	lung
24	chr11:65977800-65989400	Strong transcription	Adipose Nuclei	Adipose
25	chr11:65977800-65989800	Strong transcription	Primary T cells from cord blood	blood
26	chr11:65977800-65990000	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:65978000-65989200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr11:65978000-65989400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:65978000-65989800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:65978000-65993000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:65978800-65989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:65979600-65987000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:65979600-65989800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:65979800-66001200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr11:65980000-65994000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:65980400-65989200	Strong transcription	Primary B cells from cord blood	blood
37	chr11:65980600-65988400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:65980600-65988600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:65980600-65988800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:65981200-65990200	Weak transcription	Fetal Kidney	kidney
41	chr11:65982000-65988800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr11:65982000-65989000	Strong transcription	Esophagus	oesophagus
43	chr11:65982200-65989000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:65982200-65995800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:65982400-65989000	Strong transcription	Osteobl	bone
46	chr11:65982600-65989200	Strong transcription	A549	lung
47	chr11:65982800-65988800	Strong transcription	Ovary	ovary
48	chr11:65982800-65988800	Strong transcription	Pancreas	Pancrea
49	chr11:65982800-65989000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:65982800-65989400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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