Variant report

Variant	rs7869959
Chromosome Location	chr9:99983513-99983514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTSL2-4	chr9:99983312-99983538	ENSG00000159712.9

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10116019	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10119245	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10122063	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10125198	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10435868	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10448274	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10759522	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10817170	0.80[EUR][1000 genomes]
rs10817173	0.82[EUR][1000 genomes]
rs10817265	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10980874	0.82[EUR][1000 genomes]
rs10981209	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10981296	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10981329	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10981438	0.80[EUR][1000 genomes]
rs10981890	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11562326	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11581	0.86[JPT][hapmap]
rs11791310	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11794422	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11998999	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12003313	0.82[EUR][1000 genomes]
rs12004930	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12005128	0.84[EUR][1000 genomes]
rs12235305	0.80[EUR][1000 genomes]
rs12235734	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13297670	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13298346	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13299029	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13299627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs13301357	0.88[EUR][1000 genomes]
rs13302699	0.83[EUR][1000 genomes]
rs1544203	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs1857083	0.84[EUR][1000 genomes]
rs1903635	0.81[JPT][hapmap]
rs1947717	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2169456	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2219664	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2242187	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2306097	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2374923	0.84[EUR][1000 genomes]
rs2493442	0.87[CHB][hapmap]
rs2502644	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2615143	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2615145	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2795367	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs2818238	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2818243	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28846196	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3214072	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs34382632	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35609998	0.80[EUR][1000 genomes]
rs3747489	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3747493	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3747496	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3957904	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3994556	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4014783	0.83[EUR][1000 genomes]
rs4014789	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4145255	0.80[EUR][1000 genomes]
rs4237189	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4284138	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4313271	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4366181	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4452918	0.84[EUR][1000 genomes]
rs4523385	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4626726	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4743072	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4743076	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4743077	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4743084	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs55694850	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62556614	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478020	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6478095	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7020393	0.91[JPT][hapmap]
rs7022475	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7031789	0.82[EUR][1000 genomes]
rs7042707	0.91[JPT][hapmap]
rs713066	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs72747776	0.83[EUR][1000 genomes]
rs750674	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7850392	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7850429	0.91[AMR][1000 genomes]
rs7850504	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7855366	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7855622	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7868440	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7868563	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7868806	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869509	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869568	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869587	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7869959	VN1R51P	cis	Thyroid	GTEx
rs7869959	ANKRD18CP	cis	Thyroid	GTEx
rs7869959	RP11-520B13.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99976600-99985000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr9:99976600-99985000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:99976800-99985200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:99976800-99985400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr9:99981400-99985000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:99981800-99985000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr9:99982000-99985000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr9:99982000-99985200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:99982200-99985200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr9:99982400-99985200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:99983000-99984000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:99983000-99984400	Bivalent/Poised TSS	NHEK	skin
13	chr9:99983000-99984800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:99983000-99985000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:99983000-99985000	Active TSS	Brain Anterior Caudate	brain
16	chr9:99983000-99985200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr9:99983000-99985200	Bivalent Enhancer	Fetal Brain Male	brain
18	chr9:99983200-99983600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:99983200-99983600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:99983200-99983600	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr9:99983200-99983600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
22	chr9:99983200-99983600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr9:99983200-99983600	Bivalent Enhancer	Esophagus	oesophagus
24	chr9:99983200-99983600	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr9:99983200-99983600	Enhancers	Ovary	ovary
26	chr9:99983200-99983600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
27	chr9:99983200-99983800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:99983200-99983800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
29	chr9:99983200-99983800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:99983200-99983800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:99983200-99983800	Bivalent Enhancer	Fetal Heart	heart
32	chr9:99983200-99983800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
33	chr9:99983200-99983800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr9:99983200-99984000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:99983200-99984000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:99983200-99984000	Enhancers	Spleen	Spleen
37	chr9:99983200-99984200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr9:99983200-99984200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:99983200-99984200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr9:99983200-99984200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
41	chr9:99983200-99984400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
42	chr9:99983200-99984400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
43	chr9:99983200-99984400	Bivalent Enhancer	Fetal Stomach	stomach
44	chr9:99983200-99984400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
45	chr9:99983200-99984400	Flanking Bivalent TSS/Enh	HMEC	breast
46	chr9:99983200-99984400	Bivalent/Poised TSS	HSMM	muscle
47	chr9:99983200-99984600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:99983200-99984600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr9:99983200-99984600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:99983200-99984600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain

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