Variant report

Variant	rs12918797
Chromosome Location	chr16:75493810-75493811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75492483..75495341-chr16:75495841..75499470,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHST6-1	chr16:75493788-75493915	ENSG00000261476.1

Variant related genes	Relation type
ENSG00000166822	Chromatin interaction
ENSG00000261717	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs100912	0.86[ASN][1000 genomes]
rs1030261	0.97[ASN][1000 genomes]
rs1030262	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10871311	0.80[ASN][1000 genomes]
rs10871312	0.97[ASN][1000 genomes]
rs10871313	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11149831	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11641249	0.96[ASN][1000 genomes]
rs11641430	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11641801	0.80[ASN][1000 genomes]
rs11643207	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644306	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11644639	0.80[ASN][1000 genomes]
rs11648176	0.80[ASN][1000 genomes]
rs11649638	0.97[ASN][1000 genomes]
rs11862582	0.82[AFR][1000 genomes]
rs11865296	0.83[ASN][1000 genomes]
rs12051137	0.95[ASN][1000 genomes]
rs12149063	0.80[ASN][1000 genomes]
rs12444589	0.80[ASN][1000 genomes]
rs12446877	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12448829	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12924333	0.94[ASN][1000 genomes]
rs12927562	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12928036	0.96[ASN][1000 genomes]
rs12929673	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12932606	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12933281	0.96[ASN][1000 genomes]
rs1424013	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542864	0.81[ASN][1000 genomes]
rs17696831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834013	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834014	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161684	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs247454	0.88[ASN][1000 genomes]
rs2738809	0.88[ASN][1000 genomes]
rs2738812	0.82[ASN][1000 genomes]
rs2738813	0.82[ASN][1000 genomes]
rs2738814	0.83[ASN][1000 genomes]
rs28558946	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2865528	0.80[ASN][1000 genomes]
rs28655617	0.95[ASN][1000 genomes]
rs3115960	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34021527	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34539062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34918083	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996006	0.93[ASN][1000 genomes]
rs35209155	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35214308	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35683383	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs37592	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37593	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37594	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37595	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37597	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs37599	0.82[ASN][1000 genomes]
rs37602	0.82[ASN][1000 genomes]
rs37605	0.81[ASN][1000 genomes]
rs37606	0.96[ASN][1000 genomes]
rs40446	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887825	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4887829	0.97[ASN][1000 genomes]
rs4888415	0.80[ASN][1000 genomes]
rs4888425	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4888426	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4888427	0.94[ASN][1000 genomes]
rs4888430	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888431	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888432	0.87[ASN][1000 genomes]
rs56004344	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56116092	0.94[ASN][1000 genomes]
rs59155720	0.94[ASN][1000 genomes]
rs59347518	0.92[ASN][1000 genomes]
rs59465235	0.96[ASN][1000 genomes]
rs62060550	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62060551	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188604	0.80[ASN][1000 genomes]
rs7191890	0.83[ASN][1000 genomes]
rs7193828	0.89[ASN][1000 genomes]
rs7194035	0.89[ASN][1000 genomes]
rs7195161	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198873	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7199062	0.93[ASN][1000 genomes]
rs7199132	0.80[ASN][1000 genomes]
rs7200053	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7202596	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7204984	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7206665	0.93[ASN][1000 genomes]
rs8055490	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8055974	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8056141	0.83[ASN][1000 genomes]
rs8057084	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8063068	0.96[ASN][1000 genomes]
rs977985	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs977986	0.81[ASN][1000 genomes]
rs977987	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9923834	0.81[ASN][1000 genomes]
rs9933255	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12918797	RP11-252K23.2	cis	lung	GTEx
rs12918797	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs12918797	RP11-252K23.2	cis	Thyroid	GTEx
rs12918797	RP11-252K23.2	cis	Artery Tibial	GTEx
rs12918797	RP11-252K23.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75468800-75497000	Weak transcription	NHLF	lung
2	chr16:75469400-75497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:75469400-75497400	Weak transcription	Psoas Muscle	Psoas
4	chr16:75473600-75496000	Weak transcription	HMEC	breast
5	chr16:75477400-75494400	Weak transcription	NH-A	brain
6	chr16:75477800-75497000	Weak transcription	NHDF-Ad	bronchial
7	chr16:75481800-75497600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr16:75482400-75494200	Weak transcription	GM12878-XiMat	blood
9	chr16:75483200-75495800	Weak transcription	Fetal Brain Male	brain
10	chr16:75483600-75494200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:75483800-75496000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr16:75484000-75496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr16:75484000-75496800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr16:75485000-75494400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr16:75485400-75496800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:75485600-75494200	Weak transcription	Brain Germinal Matrix	brain
17	chr16:75485600-75495800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr16:75485600-75496400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr16:75485600-75497200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:75485800-75494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr16:75485800-75494200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr16:75485800-75494400	Weak transcription	Primary T cells from cord blood	blood
23	chr16:75485800-75494400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr16:75485800-75494600	Weak transcription	Brain Substantia Nigra	brain
25	chr16:75485800-75494600	Weak transcription	Hela-S3	cervix
26	chr16:75485800-75495200	Weak transcription	Dnd41	blood
27	chr16:75485800-75496000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr16:75485800-75496400	Weak transcription	Primary B cells from cord blood	blood
29	chr16:75485800-75496400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr16:75485800-75496800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr16:75485800-75496800	Weak transcription	Fetal Kidney	kidney
32	chr16:75485800-75496800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr16:75485800-75497000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr16:75485800-75497000	Weak transcription	Fetal Thymus	thymus
35	chr16:75485800-75497000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr16:75485800-75497200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr16:75485800-75497400	Weak transcription	Fetal Brain Female	brain
38	chr16:75485800-75497600	Weak transcription	Aorta	Aorta
39	chr16:75486000-75494200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr16:75486000-75494200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:75486000-75496800	Weak transcription	Thymus	Thymus
42	chr16:75486400-75496800	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr16:75487000-75495600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr16:75487200-75494800	Weak transcription	Brain Hippocampus Middle	brain
45	chr16:75487200-75496600	Weak transcription	HUVEC	blood vessel
46	chr16:75488000-75494400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr16:75488200-75495400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr16:75489000-75496800	Weak transcription	K562	blood
49	chr16:75489400-75495400	Enhancers	Small Intestine	intestine
50	chr16:75489800-75497400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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