Variant report

Variant	rs10514213
Chromosome Location	chr5:80526919-80526920
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACOT12-8	chr5:80521955-80529138	NONHSAT102436

Extended variants
information (count: 47 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10038684	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10041063	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10053706	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10055063	0.82[EUR][1000 genomes]
rs10066296	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10078279	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10474656	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514215	0.81[CEU][hapmap]
rs1055383	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10942945	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950033	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13362314	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1566432	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294418	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17294956	0.81[CEU][hapmap]
rs2270823	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28464111	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28650401	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2897389	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2897390	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704707	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704708	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704710	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704712	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704715	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704720	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59132806	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60488995	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60904680	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61244991	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6866499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6885028	1.00[CHB][hapmap]
rs6893467	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73130869	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7381116	0.83[AMR][1000 genomes]
rs7448717	0.88[CEU][hapmap]
rs750728	0.81[CEU][hapmap]
rs7709071	1.00[CHB][hapmap]
rs7709149	1.00[CHB][hapmap]
rs7720009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7728465	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734902	1.00[CHB][hapmap]
rs921928	1.00[CHB][hapmap]
rs9293841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10514213	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs10514213	CTC-281B15.1	cis	Stomach	GTEx
rs10514213	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs10514213	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs10514213	CTC-281B15.1	cis	Thyroid	GTEx
rs10514213	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs10514213	CTC-281B15.1	cis	lung	GTEx
rs10514213	CKMT2	cis	normal skin	skin_eQTL
rs10514213	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs10514213	CTD-2248H3.1	cis	lung	GTEx
rs10514213	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs10514213	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs10514213	CTC-281B15.1	cis	Artery Aorta	GTEx
rs10514213	CTD-2248H3.1	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80464200-80528400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:80465200-80528200	Weak transcription	Ovary	ovary
3	chr5:80491000-80528400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:80491200-80530000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:80491400-80528400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:80492000-80528600	Weak transcription	Left Ventricle	heart
7	chr5:80498000-80528800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:80498800-80530000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:80505400-80527800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:80506000-80530000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:80506400-80528000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:80507600-80528200	Weak transcription	HepG2	liver
13	chr5:80509000-80528400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:80509200-80528800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:80509400-80530000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:80510600-80528800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:80516400-80528600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:80519800-80527400	Weak transcription	Brain Substantia Nigra	brain
19	chr5:80520600-80530200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:80520800-80527200	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:80521000-80528600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr5:80522400-80530000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:80522600-80528800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:80522600-80530400	Weak transcription	Primary T cells from cord blood	blood
25	chr5:80522800-80528200	Weak transcription	Adipose Nuclei	Adipose
26	chr5:80523200-80528800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:80524200-80528200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:80524200-80528400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:80525400-80527000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:80525800-80528200	Weak transcription	Brain Angular Gyrus	brain
31	chr5:80525800-80531000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:80526400-80527000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr5:80526600-80531200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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