Variant report

Variant	rs7498801
Chromosome Location	chr16:65093846-65093847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1025311	0.80[JPT][hapmap]
rs1040270	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1040271	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10500508	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1079008	0.93[JPT][hapmap]
rs12935138	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1356823	0.89[ASN][1000 genomes]
rs1520229	0.87[JPT][hapmap]
rs1520230	0.87[JPT][hapmap]
rs1520231	0.93[JPT][hapmap]
rs1520232	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1520234	0.87[JPT][hapmap]
rs1520236	0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1520243	0.87[JPT][hapmap]
rs1532418	0.94[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs16968461	0.92[CHB][hapmap];0.90[ASN][1000 genomes]
rs16968480	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1850966	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1874457	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1915117	0.94[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2088285	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs2132543	0.85[ASN][1000 genomes]
rs2280396	1.00[CEU][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs257335	0.87[JPT][hapmap]
rs257336	0.87[JPT][hapmap]
rs257337	0.87[JPT][hapmap]
rs257341	0.80[JPT][hapmap]
rs257490	0.87[JPT][hapmap]
rs257497	0.80[JPT][hapmap]
rs257498	0.80[JPT][hapmap]
rs28216	0.88[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs34553411	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35054335	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35140	0.80[JPT][hapmap]
rs35144	0.80[JPT][hapmap]
rs35146	0.80[JPT][hapmap]
rs35148	0.80[JPT][hapmap]
rs35149	0.80[JPT][hapmap]
rs35150	0.80[JPT][hapmap]
rs35154	0.80[JPT][hapmap]
rs35176	1.00[CEU][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35188	0.80[JPT][hapmap]
rs35189	0.81[EUR][1000 genomes]
rs35191	0.80[JPT][hapmap]
rs35195	0.80[JPT][hapmap]
rs35198	0.80[JPT][hapmap]
rs35199	0.80[JPT][hapmap]
rs35200	0.80[JPT][hapmap]
rs35203	0.85[JPT][hapmap]
rs35204	0.80[JPT][hapmap]
rs35208	0.80[JPT][hapmap]
rs35210	0.80[JPT][hapmap]
rs35214	0.80[JPT][hapmap]
rs35216	0.80[JPT][hapmap]
rs35219	0.80[JPT][hapmap]
rs35709707	0.91[ASN][1000 genomes]
rs40115	0.80[JPT][hapmap]
rs40116	0.80[JPT][hapmap]
rs42863	0.80[JPT][hapmap]
rs4393595	0.93[ASN][1000 genomes]
rs4967866	0.80[JPT][hapmap]
rs4967868	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4967882	0.87[JPT][hapmap]
rs4967884	0.81[ASN][1000 genomes]
rs4967885	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4967886	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59954387	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7204729	0.94[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs8048351	0.93[ASN][1000 genomes]
rs878359	0.87[JPT][hapmap]
rs909003	0.80[JPT][hapmap]
rs973200	0.80[JPT][hapmap]
rs974782	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9935608	0.87[JPT][hapmap]

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	nsv948640	chr16:64859061-65112790	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv833260	chr16:65050647-65218759	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1831	chr16:65071976-65106105	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7498801	LRRC29	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65058600-65104400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:65069800-65105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr16:65072800-65096200	Weak transcription	Colon Smooth Muscle	Colon
4	chr16:65074400-65094000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:65081800-65094800	Weak transcription	Lung	lung
6	chr16:65083800-65100000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr16:65085000-65095800	Weak transcription	Fetal Brain Female	brain
8	chr16:65087400-65104800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr16:65087800-65100600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr16:65087800-65102000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr16:65087800-65103600	Weak transcription	Aorta	Aorta
12	chr16:65088000-65095600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr16:65088200-65101600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr16:65089400-65098000	Weak transcription	Fetal Muscle Leg	muscle
15	chr16:65089400-65101200	Weak transcription	Fetal Brain Male	brain
16	chr16:65089600-65095600	Weak transcription	HSMMtube	muscle
17	chr16:65090400-65099800	Enhancers	Brain Cingulate Gyrus	brain
18	chr16:65090800-65094800	Weak transcription	NHDF-Ad	bronchial
19	chr16:65091400-65097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr16:65091600-65095800	Weak transcription	Fetal Kidney	kidney
21	chr16:65091800-65094800	Weak transcription	NHLF	lung
22	chr16:65092000-65095800	Weak transcription	HSMM	muscle
23	chr16:65092000-65096200	Weak transcription	Ovary	ovary
24	chr16:65092000-65097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr16:65092000-65098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:65092200-65102600	Enhancers	Brain Angular Gyrus	brain
27	chr16:65092600-65095200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr16:65092800-65094400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:65093000-65094000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr16:65093000-65094200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr16:65093000-65094400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr16:65093200-65094200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:65093200-65094200	Weak transcription	Osteobl	bone
34	chr16:65093200-65094800	Weak transcription	Pancreas	Pancrea
35	chr16:65093400-65094000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr16:65093400-65099800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr16:65093600-65094600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr16:65093600-65095800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr16:65093600-65096200	Weak transcription	Brain Germinal Matrix	brain
40	chr16:65093800-65094000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr16:65093800-65094000	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr16:65093800-65094000	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr16:65093800-65094200	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr16:65093800-65094600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr16:65093800-65096000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr16:65093800-65097000	Enhancers	NH-A	brain
47	chr16:65093800-65097200	Enhancers	Fetal Lung	lung
48	chr16:65093800-65097800	Weak transcription	Fetal Stomach	stomach
49	chr16:65093800-65103600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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