Variant report

Variant	rs4647529
Chromosome Location	chr9:97876346-97876347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf3-1	chr9:97876257-97876743	ENSG00000229065.1

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10115247	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739992	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10739993	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10761377	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821451	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821453	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821454	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821455	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993490	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13295862	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17686583	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1979022	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2031599	0.80[EUR][1000 genomes]
rs2166402	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2282216	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297596	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2297597	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2404457	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3277	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34045846	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34532504	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3737142	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3780561	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3780562	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3780564	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3780567	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780568	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3824486	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3844341	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3852402	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4647382	0.83[EUR][1000 genomes]
rs4647443	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4647459	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4647462	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4647475	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4647528	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4647534	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4647554	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4647558	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744446	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744451	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479601	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7019043	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7023007	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7027204	0.82[EUR][1000 genomes]
rs7034538	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850958	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7854570	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7872648	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7874310	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs879492	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs881791	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs963774	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
3	chr9:97847600-97878400	Weak transcription	Dnd41	blood
4	chr9:97855200-97876800	Weak transcription	GM12878-XiMat	blood
5	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:97855600-97876400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:97855600-97878600	Weak transcription	Stomach Mucosa	stomach
8	chr9:97858600-97877200	Strong transcription	Fetal Intestine Large	intestine
9	chr9:97858600-97878400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:97860400-97879000	Strong transcription	Liver	Liver
11	chr9:97861200-97877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:97861200-97889800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:97863600-97883600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:97864000-97877800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr9:97865200-97876800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:97865200-97877200	Weak transcription	Small Intestine	intestine
17	chr9:97865600-97883600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:97865800-97877600	Strong transcription	Fetal Intestine Small	intestine
19	chr9:97866000-97883400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:97866000-97889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:97866200-97889600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:97866400-97886600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:97867000-97878800	Weak transcription	Right Atrium	heart
24	chr9:97867800-97877000	Strong transcription	Primary T cells from cord blood	blood
25	chr9:97868600-97889400	Weak transcription	Fetal Heart	heart
26	chr9:97869600-97878800	Weak transcription	Brain Germinal Matrix	brain
27	chr9:97869800-97877200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr9:97869800-97886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:97869800-97889800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr9:97870000-97883400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:97870200-97876600	Weak transcription	Fetal Brain Male	brain
32	chr9:97870400-97878600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:97870400-97889600	Weak transcription	Fetal Thymus	thymus
34	chr9:97870600-97889800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr9:97870800-97878800	Weak transcription	Brain Angular Gyrus	brain
36	chr9:97871600-97877000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr9:97871600-97878800	Weak transcription	Brain Substantia Nigra	brain
38	chr9:97872000-97881000	Weak transcription	NH-A	brain
39	chr9:97872400-97876400	Weak transcription	Psoas Muscle	Psoas
40	chr9:97872800-97877400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr9:97873200-97876800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:97873200-97878600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:97873600-97877000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:97873600-97877200	Strong transcription	Fetal Stomach	stomach
45	chr9:97873600-97878800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:97873800-97877000	Strong transcription	Fetal Lung	lung
47	chr9:97874200-97877400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:97874600-97878600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:97874600-97889400	Weak transcription	Colonic Mucosa	Colon
50	chr9:97874800-97881000	Weak transcription	Fetal Kidney	kidney

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