Variant report

Variant	rs10041776
Chromosome Location	chr5:114854685-114854686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10038493	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10043094	0.88[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap]
rs10053572	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10079000	0.88[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap]
rs1015812	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13184723	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13356084	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13357862	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2032842	0.83[CHB][hapmap]
rs2546484	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256938	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256977	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs256989	0.84[ASN][1000 genomes]
rs256995	0.82[ASN][1000 genomes]
rs372702	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6860557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6878790	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6892071	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6893854	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6894123	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs746566	0.88[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs766454	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326964	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.98[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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10041776	TICAM2	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114843200-114854800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:114843200-114858800	Weak transcription	Left Ventricle	heart
3	chr5:114843600-114860000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:114844000-114859000	Weak transcription	HSMMtube	muscle
5	chr5:114844200-114855000	Weak transcription	HSMM	muscle
6	chr5:114844200-114858000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:114844200-114858800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:114844200-114859800	Weak transcription	Osteobl	bone
9	chr5:114845400-114858600	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:114845600-114862400	Weak transcription	Fetal Heart	heart
11	chr5:114846400-114860000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:114846600-114858200	Weak transcription	A549	lung
13	chr5:114846600-114860000	Weak transcription	Ovary	ovary
14	chr5:114846800-114854800	Weak transcription	Dnd41	blood
15	chr5:114846800-114858600	Weak transcription	Brain Anterior Caudate	brain
16	chr5:114846800-114860000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:114847200-114858800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:114847600-114858600	Weak transcription	Primary T cells from cord blood	blood
19	chr5:114848000-114858200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:114848000-114860400	Weak transcription	Esophagus	oesophagus
21	chr5:114848400-114858600	Weak transcription	Brain Germinal Matrix	brain
22	chr5:114848400-114860200	Weak transcription	Aorta	Aorta
23	chr5:114848600-114857200	Weak transcription	GM12878-XiMat	blood
24	chr5:114848600-114860200	Weak transcription	Thymus	Thymus
25	chr5:114849000-114858600	Weak transcription	Primary B cells from cord blood	blood
26	chr5:114849200-114858200	Weak transcription	K562	blood
27	chr5:114849200-114859200	Weak transcription	HepG2	liver
28	chr5:114849400-114856800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:114849400-114858600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:114850000-114855800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:114850600-114858200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:114850800-114858000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:114851200-114858600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:114851600-114858400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr5:114851600-114858400	Weak transcription	NHLF	lung
36	chr5:114851800-114857000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:114851800-114858800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:114851800-114859000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:114852000-114858000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:114852200-114855400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr5:114852400-114858200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr5:114852600-114858400	Weak transcription	NH-A	brain
43	chr5:114852800-114858200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:114853200-114854800	Weak transcription	Liver	Liver
45	chr5:114853200-114858200	Strong transcription	NHDF-Ad	bronchial
46	chr5:114853200-114858400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:114853400-114855000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:114853400-114858600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:114853400-114858800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:114853400-114859000	Weak transcription	Rectal Mucosa Donor 29	rectum

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