Variant report

Variant	rs56386213
Chromosome Location	chr11:36291554-36291555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C11orf55-2	chr11:36290834-36293377	ENSG00000196559.3

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10836528	0.84[EUR][1000 genomes]
rs10836530	0.83[EUR][1000 genomes]
rs10836531	0.83[EUR][1000 genomes]
rs11033524	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11033527	0.85[AFR][1000 genomes]
rs11033538	0.84[EUR][1000 genomes]
rs11033542	0.80[EUR][1000 genomes]
rs11602024	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1562325	0.82[EUR][1000 genomes]
rs1562326	0.82[EUR][1000 genomes]
rs17814690	0.84[EUR][1000 genomes]
rs1900336	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2289987	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2422185	0.80[EUR][1000 genomes]
rs2422186	0.80[EUR][1000 genomes]
rs2422187	0.80[EUR][1000 genomes]
rs2901672	0.81[EUR][1000 genomes]
rs4418777	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61878683	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6484831	0.81[EUR][1000 genomes]
rs7107433	0.81[EUR][1000 genomes]
rs7109505	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72946165	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7951298	0.80[EUR][1000 genomes]
rs9667667	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9787880	0.86[AFR][1000 genomes]
rs9787894	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56386213	LINC00610	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36276800-36294400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:36278200-36292600	Weak transcription	Esophagus	oesophagus
3	chr11:36278200-36293200	Weak transcription	Fetal Lung	lung
4	chr11:36279200-36292000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:36279200-36294800	Weak transcription	HMEC	breast
6	chr11:36280400-36294800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:36280400-36299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:36280800-36292000	Weak transcription	Brain Substantia Nigra	brain
9	chr11:36280800-36300200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:36281000-36292600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:36281400-36292200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:36281400-36293200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:36282000-36292000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:36282200-36302000	Weak transcription	NHEK	skin
15	chr11:36282800-36292200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:36283000-36298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:36283200-36300000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:36286400-36293000	Weak transcription	Right Ventricle	heart
19	chr11:36287000-36294200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr11:36287600-36291800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:36287600-36295400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:36287600-36304800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:36287800-36292000	Weak transcription	Brain Anterior Caudate	brain
24	chr11:36287800-36292000	Weak transcription	Brain Germinal Matrix	brain
25	chr11:36287800-36292200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:36287800-36292400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:36287800-36292800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr11:36287800-36293400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:36288000-36293200	Weak transcription	Osteobl	bone
30	chr11:36288000-36310200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:36288200-36292000	Weak transcription	Thymus	Thymus
32	chr11:36288400-36295200	Weak transcription	NHLF	lung
33	chr11:36288400-36304600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:36288600-36293000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:36288800-36292000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:36288800-36292200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:36288800-36292200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:36289000-36292200	Weak transcription	HSMM	muscle
39	chr11:36289200-36292000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:36289200-36293000	Weak transcription	HSMMtube	muscle
41	chr11:36289200-36299800	Weak transcription	HepG2	liver
42	chr11:36289200-36300000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr11:36289400-36292200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:36289400-36292600	Weak transcription	Placenta	Placenta
45	chr11:36289400-36292600	Weak transcription	Left Ventricle	heart
46	chr11:36289400-36293600	Weak transcription	Fetal Kidney	kidney
47	chr11:36289400-36294600	Weak transcription	Fetal Brain Male	brain
48	chr11:36289600-36291800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr11:36289600-36292000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:36289600-36292000	Weak transcription	Primary B cells from peripheral blood	blood

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