Variant report

Variant	rs954439
Chromosome Location	chr10:91066460-91066461
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10159774	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs10749605	0.85[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs10749606	0.85[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs10749607	0.85[CEU][hapmap];0.84[AMR][1000 genomes]
rs1888923	0.89[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs215493	0.81[CEU][hapmap]
rs303217	0.81[CEU][hapmap]
rs304440	0.81[CEU][hapmap]
rs304449	0.81[CEU][hapmap]
rs304478	0.81[CEU][hapmap]
rs304485	0.81[CEU][hapmap]
rs304495	0.81[CEU][hapmap]
rs304504	0.81[CEU][hapmap]
rs305371	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs305373	0.80[AMR][1000 genomes]
rs305375	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs305376	0.80[AMR][1000 genomes]
rs305377	0.80[AMR][1000 genomes]
rs4933504	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4934471	0.92[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4934473	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4934475	0.85[CEU][hapmap];0.84[AMR][1000 genomes]
rs627524	0.85[CEU][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs6586184	0.82[AMR][1000 genomes]
rs7094510	0.85[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs7095398	0.85[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs975686	0.91[AMR][1000 genomes];0.87[EUR][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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv1040375	chr10:91022218-91153074	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv34085	chr10:91065949-91174175	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers 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	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs954439	FAM129C	trans	lymphoblastoid	seeQTL
rs954439	IFIT5	cis	Skin Sun Exposed Lower leg	GTEx
rs954439	LIPA	cis	parietal	SCAN
rs954439	LIPK	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91055800-91070000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:91063200-91066600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr10:91063200-91066800	Weak transcription	Osteobl	bone
4	chr10:91063200-91067000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:91063200-91074600	Weak transcription	Fetal Intestine Small	intestine
6	chr10:91063200-91076000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:91063400-91068600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:91063400-91069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr10:91063400-91072600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:91063800-91066800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:91063800-91067800	Weak transcription	Stomach Mucosa	stomach
12	chr10:91063800-91068200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:91063800-91069200	Weak transcription	Esophagus	oesophagus
14	chr10:91063800-91069200	Weak transcription	Pancreas	Pancrea
15	chr10:91063800-91069200	Weak transcription	Right Atrium	heart
16	chr10:91063800-91070400	Weak transcription	Fetal Kidney	kidney
17	chr10:91063800-91074200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr10:91064000-91072800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr10:91064200-91067800	Weak transcription	Small Intestine	intestine
20	chr10:91064200-91086600	Weak transcription	Hela-S3	cervix
21	chr10:91065200-91067600	Enhancers	HSMM	muscle
22	chr10:91065400-91066600	Genic enhancers	Brain Angular Gyrus	brain
23	chr10:91065400-91066800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr10:91065400-91067800	Enhancers	HSMMtube	muscle
25	chr10:91065400-91068800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr10:91065400-91069800	Strong transcription	Primary B cells from cord blood	blood
27	chr10:91065600-91066600	Strong transcription	Fetal Thymus	thymus
28	chr10:91065600-91067000	Genic enhancers	Brain Hippocampus Middle	brain
29	chr10:91065600-91067200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr10:91065600-91067400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr10:91065600-91067400	Enhancers	Fetal Brain Male	brain
32	chr10:91065600-91067800	Strong transcription	Primary hematopoietic stem cells	blood
33	chr10:91065600-91067800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr10:91065600-91067800	Strong transcription	Fetal Lung	lung
35	chr10:91065600-91068000	Strong transcription	Primary T cells from cord blood	blood
36	chr10:91065600-91068400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr10:91065600-91069200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr10:91065600-91069400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr10:91065600-91069400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr10:91065600-91069400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr10:91065800-91066600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr10:91065800-91066600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr10:91065800-91066600	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr10:91065800-91066600	Strong transcription	NHDF-Ad	bronchial
45	chr10:91065800-91066800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr10:91065800-91066800	Strong transcription	Lung	lung
47	chr10:91065800-91066800	Strong transcription	Dnd41	blood
48	chr10:91065800-91067000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:91065800-91067000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:91065800-91067000	Strong transcription	Duodenum Mucosa	Duodenum

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