Variant report

Variant	rs12235734
Chromosome Location	chr9:99983312-99983313
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: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10116019	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10119245	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10759522	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10817170	0.80[EUR][1000 genomes]
rs10817173	0.82[EUR][1000 genomes]
rs10817265	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10980874	0.82[EUR][1000 genomes]
rs10981209	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981280	0.81[CHB][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981288	0.82[CHB][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981296	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10981329	0.82[CHB][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981438	0.80[EUR][1000 genomes]
rs11562326	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11791310	0.82[CHB][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11794422	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11998999	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12003313	0.82[EUR][1000 genomes]
rs12004930	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12005128	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12235305	0.80[EUR][1000 genomes]
rs13297670	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13298346	0.82[CHB][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13299029	0.82[EUR][1000 genomes]
rs13299627	0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs13301357	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13302699	0.83[EUR][1000 genomes]
rs1544203	0.80[EUR][1000 genomes]
rs1857083	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2374923	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2795367	0.80[EUR][1000 genomes]
rs28846196	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34382632	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35609998	0.80[EUR][1000 genomes]
rs3957904	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3994556	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4014783	0.83[EUR][1000 genomes]
rs4014789	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4014790	0.80[ASN][1000 genomes]
rs4145255	0.80[EUR][1000 genomes]
rs4284138	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4452918	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4626726	0.88[EUR][1000 genomes]
rs55694850	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62556614	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478020	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7020393	0.80[ASN][1000 genomes]
rs7022475	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7031789	0.82[EUR][1000 genomes]
rs7042707	0.81[ASN][1000 genomes]
rs72747776	0.83[EUR][1000 genomes]
rs7850392	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7850429	0.82[AMR][1000 genomes]
rs7850504	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7855366	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7855622	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7866267	0.80[ASN][1000 genomes]
rs7868440	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7868563	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7868806	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869509	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869568	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869587	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869959	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv972433	chr9:99962059-99983443	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12235734	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

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	chr9:99982400-99983400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:99982400-99985200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:99983000-99983400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr9:99983000-99983400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
14	chr9:99983000-99983400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:99983000-99983400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:99983000-99983400	Bivalent Enhancer	Colon Smooth Muscle	Colon
17	chr9:99983000-99984000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:99983000-99984400	Bivalent/Poised TSS	NHEK	skin
19	chr9:99983000-99984800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:99983000-99985000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:99983000-99985000	Active TSS	Brain Anterior Caudate	brain
22	chr9:99983000-99985200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr9:99983000-99985200	Bivalent Enhancer	Fetal Brain Male	brain
24	chr9:99983200-99983400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
25	chr9:99983200-99983400	Bivalent Enhancer	Primary B cells from cord blood	blood
26	chr9:99983200-99983400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr9:99983200-99983400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
28	chr9:99983200-99983400	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:99983200-99983400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
30	chr9:99983200-99983400	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:99983200-99983400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:99983200-99983400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:99983200-99983400	Bivalent Enhancer	Adipose Nuclei	Adipose
34	chr9:99983200-99983400	Bivalent Enhancer	Liver	Liver
35	chr9:99983200-99983400	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr9:99983200-99983400	Bivalent Enhancer	Brain Germinal Matrix	brain
37	chr9:99983200-99983400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
38	chr9:99983200-99983400	Bivalent/Poised TSS	Colonic Mucosa	Colon
39	chr9:99983200-99983400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
40	chr9:99983200-99983400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
41	chr9:99983200-99983400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr9:99983200-99983400	Bivalent Enhancer	Left Ventricle	heart
43	chr9:99983200-99983400	Enhancers	Pancreas	Pancrea
44	chr9:99983200-99983400	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
45	chr9:99983200-99983400	Bivalent Enhancer	Psoas Muscle	Psoas
46	chr9:99983200-99983400	Bivalent Enhancer	Rectal Smooth Muscle	rectum
47	chr9:99983200-99983400	Flanking Active TSS	Right Atrium	heart
48	chr9:99983200-99983400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr9:99983200-99983400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
50	chr9:99983200-99983400	Bivalent Enhancer	NH-A	brain

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