Variant report

Variant	rs964051
Chromosome Location	chr4:77199414-77199415
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STBD1-2	chr4:77199222-77199808	NONHSAT096993

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11097313	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11097314	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11933305	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11946806	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643334	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13119644	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13122345	0.89[CHB][hapmap]
rs13123108	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13151765	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441909	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441910	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441913	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441914	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1530296	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530297	0.83[JPT][hapmap]
rs1530298	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1583944	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17236158	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17308336	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1876536	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1876537	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1876538	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876539	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876540	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1876541	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1876542	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876543	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1969148	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1969149	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2869870	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869871	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733250	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733253	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821980	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859439	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859440	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4859441	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859650	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859651	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859654	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859655	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859656	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859657	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59864739	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60397621	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60876302	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61595008	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6823078	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs736634	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs736636	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7665023	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs768979	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7699714	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv461559	chr4:77192838-77204500	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594695	chr4:77192838-77204500	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs964051	FAM47E	cis	Thyroid	GTEx
rs964051	CCDC158	cis	parietal	SCAN
rs964051	FAM47E	cis	cerebellum	SCAN
rs964051	FAM47E	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77173600-77202000	Weak transcription	Psoas Muscle	Psoas
2	chr4:77173800-77215800	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:77178800-77201200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:77180000-77202000	Weak transcription	Gastric	stomach
5	chr4:77186400-77204200	Weak transcription	Aorta	Aorta
6	chr4:77186600-77215000	Weak transcription	Brain Anterior Caudate	brain
7	chr4:77187600-77202000	Weak transcription	Brain Substantia Nigra	brain
8	chr4:77188000-77202200	Weak transcription	Brain Angular Gyrus	brain
9	chr4:77188200-77202000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:77192600-77212200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:77193000-77201800	Weak transcription	Left Ventricle	heart
12	chr4:77193000-77202000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:77193000-77202200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:77194000-77204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:77194200-77216400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:77195000-77200200	Enhancers	HepG2	liver
17	chr4:77195800-77200400	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr4:77196200-77199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:77198200-77201400	Weak transcription	Pancreas	Pancrea
20	chr4:77198200-77201600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:77198600-77200400	Enhancers	Adipose Nuclei	Adipose
22	chr4:77198800-77199600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:77198800-77200200	Enhancers	Stomach Mucosa	stomach
24	chr4:77198800-77200400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:77199000-77200200	Enhancers	A549	lung
26	chr4:77199000-77200400	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr4:77199200-77199600	Enhancers	Small Intestine	intestine
28	chr4:77199200-77199800	Enhancers	Placenta	Placenta
29	chr4:77199400-77199800	Flanking Active TSS	Liver	Liver
30	chr4:77199400-77200000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr4:77199400-77200000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr4:77199400-77200200	Enhancers	Fetal Intestine Large	intestine
33	chr4:77199400-77200200	Enhancers	Fetal Intestine Small	intestine
34	chr4:77199400-77201400	Weak transcription	Duodenum Mucosa	Duodenum

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