Variant report

Variant	rs34905303
Chromosome Location	chr9:100138388-100138389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDRD7-1	chr9:100137736-100140806	NONHSAT133501

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1048451	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10521029	0.83[EUR][1000 genomes]
rs10817384	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817491	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817504	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10981434	0.82[EUR][1000 genomes]
rs10981444	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10981460	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10981688	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981701	0.91[AMR][1000 genomes]
rs10981784	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981800	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981801	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123379	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11581	1.00[EUR][1000 genomes]
rs12115447	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12115448	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12377538	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12378350	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12550923	0.82[EUR][1000 genomes]
rs12551740	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12551818	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12552101	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12552659	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12553155	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12553213	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12553259	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12554363	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12555277	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13285567	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13286510	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13289813	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13292715	0.82[EUR][1000 genomes]
rs13300328	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13301045	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13301965	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1531440	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1564048	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1564050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919506	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16919656	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16919661	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16919671	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16919675	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2045729	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2045730	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045731	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279113	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2290933	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2306090	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306092	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306094	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2401384	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34135027	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34183765	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34355647	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34476799	0.82[EUR][1000 genomes]
rs34564795	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34609282	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34616426	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34754033	0.86[EUR][1000 genomes]
rs34870571	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34954690	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35066943	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123877	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35534888	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35623544	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35737497	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35778461	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35778718	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35788892	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747490	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747491	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747492	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747495	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3747498	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747499	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747504	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747506	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3747507	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747510	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747511	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3827484	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827485	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3994560	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41316960	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4742686	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742688	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743069	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743070	0.82[EUR][1000 genomes]
rs4743073	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743082	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743083	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743085	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743086	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60681062	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62557460	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62557461	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62557462	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62557463	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62559861	0.83[EUR][1000 genomes]
rs6478038	0.84[EUR][1000 genomes]
rs6478039	0.84[EUR][1000 genomes]
rs7020530	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7038496	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7041222	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73565808	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7872669	0.85[EUR][1000 genomes]
rs7874652	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898869	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898870	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9696058	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34905303	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100077000-100140800	Weak transcription	Fetal Brain Male	brain
2	chr9:100091600-100149200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr9:100104400-100142000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:100106800-100143200	Weak transcription	Liver	Liver
5	chr9:100107200-100138400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:100108000-100148200	Weak transcription	Esophagus	oesophagus
7	chr9:100115400-100144600	Weak transcription	Hela-S3	cervix
8	chr9:100115600-100139200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:100117400-100145000	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:100117600-100146400	Weak transcription	Small Intestine	intestine
11	chr9:100118200-100141600	Weak transcription	Primary T cells from cord blood	blood
12	chr9:100126600-100141600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr9:100126600-100148400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:100127000-100148600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:100129000-100144400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:100129600-100138600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:100132000-100140000	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr9:100132000-100142600	Weak transcription	Fetal Kidney	kidney
19	chr9:100132000-100149000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:100132200-100140200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:100132200-100141000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr9:100132200-100141400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr9:100132400-100138400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:100132400-100140000	Strong transcription	Right Ventricle	heart
25	chr9:100132400-100140600	Weak transcription	Fetal Heart	heart
26	chr9:100132400-100141000	Strong transcription	Adipose Nuclei	Adipose
27	chr9:100132400-100146800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:100132600-100139400	Strong transcription	Fetal Muscle Leg	muscle
29	chr9:100132600-100144400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:100132600-100146800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:100132600-100148600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:100132600-100149400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:100132600-100149400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:100132800-100139400	Weak transcription	Primary B cells from cord blood	blood
35	chr9:100132800-100141200	Strong transcription	Fetal Stomach	stomach
36	chr9:100133000-100138600	Weak transcription	Brain Germinal Matrix	brain
37	chr9:100133000-100141000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:100133200-100139200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:100133400-100140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:100133400-100148400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:100134000-100142200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr9:100134000-100144400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:100134600-100148600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:100135800-100140000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:100135800-100141200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:100136000-100141400	Strong transcription	Brain Hippocampus Middle	brain
47	chr9:100136000-100142400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr9:100136200-100139800	Strong transcription	Fetal Intestine Small	intestine
49	chr9:100136200-100140000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr9:100136600-100142800	Weak transcription	Duodenum Mucosa	Duodenum

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