Variant report

Variant	rs1095999
Chromosome Location	chr12:51367350-51367351
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51365371..51368263-chr12:51372019..51374890,3	K562	blood:
2	chr12:51365539..51368263-chr12:51371377..51373519,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10275	0.82[EUR][1000 genomes]
rs10783409	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876127	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876128	0.83[EUR][1000 genomes]
rs10876129	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876130	0.84[EUR][1000 genomes]
rs10876131	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876132	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169657	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169695	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12424509	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12427345	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1486014	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs15756	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1632791	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17125111	1.00[ASN][1000 genomes]
rs2029145	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2029146	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs224448	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs224572	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544019	0.80[EUR][1000 genomes]
rs2554863	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630370	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2630371	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370462	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs427020	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768947	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874804	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61934800	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580782	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs706805	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135399	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7136960	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976431	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7977740	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829015	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs829025	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9739342	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1053466	chr12:51350285-51375969	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1095999	LETMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
2	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
3	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
4	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:51331600-51373800	Weak transcription	Pancreas	Pancrea
6	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:51331800-51382000	Weak transcription	Ovary	ovary
8	chr12:51341600-51378200	Weak transcription	Right Ventricle	heart
9	chr12:51341800-51372600	Weak transcription	Osteobl	bone
10	chr12:51341800-51383200	Weak transcription	Fetal Brain Male	brain
11	chr12:51342400-51373200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:51342800-51378400	Weak transcription	NHLF	lung
13	chr12:51344000-51382000	Weak transcription	Esophagus	oesophagus
14	chr12:51344600-51381600	Weak transcription	Spleen	Spleen
15	chr12:51347200-51378000	Weak transcription	Brain Angular Gyrus	brain
16	chr12:51347400-51378000	Weak transcription	Brain Anterior Caudate	brain
17	chr12:51350800-51380600	Weak transcription	Fetal Lung	lung
18	chr12:51354400-51383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:51355600-51378000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:51355800-51378000	Weak transcription	A549	lung
21	chr12:51356000-51372600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:51357600-51378000	Weak transcription	Psoas Muscle	Psoas
23	chr12:51358800-51377800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:51359800-51380400	Weak transcription	Fetal Kidney	kidney
25	chr12:51360200-51374400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr12:51360200-51381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:51360400-51372600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:51360400-51374400	Weak transcription	HUVEC	blood vessel
29	chr12:51360600-51381000	Weak transcription	Primary B cells from cord blood	blood
30	chr12:51360600-51381800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:51361600-51382200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:51362200-51372600	Weak transcription	Adipose Nuclei	Adipose
33	chr12:51362200-51373400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:51362200-51373800	Weak transcription	Placenta	Placenta
35	chr12:51362400-51376800	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:51362400-51378600	Weak transcription	NH-A	brain
37	chr12:51362400-51382000	Weak transcription	Lung	lung
38	chr12:51362600-51378000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:51362800-51384400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:51363400-51373800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:51363400-51384000	Weak transcription	Colonic Mucosa	Colon
42	chr12:51363600-51381200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:51363800-51372600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:51364000-51372400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:51364000-51380400	Weak transcription	K562	blood
46	chr12:51364600-51378400	Weak transcription	Colon Smooth Muscle	Colon
47	chr12:51364600-51384400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr12:51365600-51374200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:51365800-51374200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:51365800-51374800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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