Variant report

Variant	rs1052654
Chromosome Location	chr8:42885355-42885356
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HOOK3-1	chr8:42883692-42885673	NONHSAT126320

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11984732	1.00[ASW][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap]
rs11986681	0.92[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11987893	0.91[ASW][hapmap];0.91[CEU][hapmap];0.86[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11990515	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11992567	0.91[LWK][hapmap]
rs11997799	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13248091	0.84[CEU][hapmap]
rs13251524	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13252221	0.84[CEU][hapmap]
rs13256221	0.84[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs13257298	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13260731	0.84[CEU][hapmap]
rs13269584	0.84[CEU][hapmap];1.00[MEX][hapmap]
rs13271956	0.84[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs13282019	0.84[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs16891663	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16891667	0.84[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs17622577	0.84[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs17622732	0.84[CEU][hapmap];1.00[MEX][hapmap]
rs2376493	0.81[ASW][hapmap]
rs34100417	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34143633	0.84[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs34152125	0.84[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs34210297	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs34242561	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs34489103	0.81[ASW][hapmap]
rs34864660	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35252795	0.91[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35390123	0.84[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs35688388	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36026629	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs57652067	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57797146	0.94[AFR][1000 genomes]
rs58729413	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60292433	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62515942	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62515949	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62517585	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6996034	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6999489	0.91[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7004940	0.90[AFR][1000 genomes]
rs7010367	0.81[AFR][1000 genomes]
rs7014595	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71521601	0.82[AMR][1000 genomes]
rs73629163	0.86[AFR][1000 genomes]
rs7462864	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7820326	0.85[YRI][hapmap]
rs7821062	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7829867	0.91[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7838845	0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890846	chr8:42625663-43240123	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1024688	chr8:42709414-43333639	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv539563	chr8:42709414-43333639	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1033927	chr8:42748842-43575771	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv533812	chr8:42755447-43528350	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv1032781	chr8:42772394-43461484	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
7	nsv1021281	chr8:42807619-43472678	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	nsv429912	chr8:42852444-43701143	ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
9	nsv869499	chr8:42858608-43541986	Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
10	nsv916847	chr8:42858611-43541984	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS 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	81 gene(s)	inside rSNPs	diseases
11	nsv1027779	chr8:42863024-43729296	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1052654	FNTA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:42847000-42889400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:42847200-42886800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr8:42859000-42891600	Weak transcription	Small Intestine	intestine
4	chr8:42864000-42889400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr8:42866000-42889400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:42866200-42889600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:42867200-42889400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr8:42868000-42889400	Weak transcription	NHEK	skin
9	chr8:42868000-42891600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:42870200-42890800	Weak transcription	Fetal Brain Male	brain
11	chr8:42873200-42889600	Weak transcription	Aorta	Aorta
12	chr8:42873800-42887600	Weak transcription	HepG2	liver
13	chr8:42873800-42889400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:42873800-42889400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr8:42873800-42889400	Weak transcription	Ovary	ovary
16	chr8:42873800-42889400	Weak transcription	Thymus	Thymus
17	chr8:42873800-42889400	Weak transcription	Spleen	Spleen
18	chr8:42873800-42891000	Weak transcription	NHLF	lung
19	chr8:42873800-42891400	Weak transcription	Esophagus	oesophagus
20	chr8:42873800-42891800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr8:42873800-42892200	Weak transcription	Gastric	stomach
22	chr8:42874000-42886800	Weak transcription	GM12878-XiMat	blood
23	chr8:42874200-42891400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr8:42874600-42889600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr8:42875000-42889400	Weak transcription	Brain Angular Gyrus	brain
26	chr8:42875000-42889600	Weak transcription	HMEC	breast
27	chr8:42875000-42891200	Weak transcription	Fetal Kidney	kidney
28	chr8:42875200-42886600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr8:42875600-42891800	Weak transcription	Colon Smooth Muscle	Colon
30	chr8:42875800-42889400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr8:42875800-42889600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr8:42876000-42889600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr8:42876000-42889600	Weak transcription	Pancreas	Pancrea
34	chr8:42876000-42891000	Weak transcription	NHDF-Ad	bronchial
35	chr8:42876000-42891200	Weak transcription	Psoas Muscle	Psoas
36	chr8:42876000-42892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr8:42876200-42889400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr8:42876200-42889600	Weak transcription	Brain Anterior Caudate	brain
39	chr8:42876200-42891000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr8:42876200-42891400	Weak transcription	Left Ventricle	heart
41	chr8:42876400-42891400	Weak transcription	HUVEC	blood vessel
42	chr8:42876400-42891600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr8:42876400-42891800	Weak transcription	NH-A	brain
44	chr8:42876600-42889400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr8:42876600-42889400	Weak transcription	Brain Germinal Matrix	brain
46	chr8:42876600-42889400	Weak transcription	Lung	lung
47	chr8:42876600-42889600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:42876600-42895200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr8:42877000-42889400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr8:42877600-42885400	Weak transcription	Rectal Mucosa Donor 29	rectum

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