Variant report

Variant	rs7662296
Chromosome Location	chr4:151074532-151074533
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10001334	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10001645	0.80[CEU][hapmap]
rs10001651	0.80[CEU][hapmap]
rs11723944	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737128	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814207	0.85[CEU][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28366470	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420313	0.85[EUR][1000 genomes]
rs28530482	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28589304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28632044	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28646031	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687892	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4353883	0.80[CEU][hapmap]
rs56849087	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60907583	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62338191	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535715	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6535716	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6826837	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670292	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7683407	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884660	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7662296	TLR2	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151045200-151099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:151064600-151080200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:151069600-151075400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:151070800-151080600	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:151071400-151091400	Weak transcription	Osteobl	bone
6	chr4:151071600-151080400	Weak transcription	NHLF	lung
7	chr4:151071600-151091600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:151072200-151074800	Weak transcription	Right Ventricle	heart
9	chr4:151072600-151077200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:151072600-151088000	Weak transcription	Fetal Stomach	stomach
11	chr4:151072600-151089000	Weak transcription	Aorta	Aorta
12	chr4:151073600-151074600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:151073600-151074600	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr4:151073600-151074600	Enhancers	A549	lung
15	chr4:151073800-151075400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:151074000-151074600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr4:151074000-151074600	Enhancers	Brain Substantia Nigra	brain
18	chr4:151074000-151074800	Enhancers	Rectal Smooth Muscle	rectum
19	chr4:151074000-151075000	Enhancers	Brain Cingulate Gyrus	brain
20	chr4:151074000-151077200	Enhancers	Fetal Heart	heart
21	chr4:151074200-151074600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr4:151074200-151074600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:151074200-151074600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:151074200-151074600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:151074200-151074600	Enhancers	Brain Anterior Caudate	brain
26	chr4:151074200-151074600	Enhancers	HSMM	muscle
27	chr4:151074200-151074600	Enhancers	HSMMtube	muscle
28	chr4:151074200-151074600	Enhancers	NHDF-Ad	bronchial
29	chr4:151074200-151074800	Enhancers	Brain Hippocampus Middle	brain
30	chr4:151074200-151075200	Enhancers	Left Ventricle	heart
31	chr4:151074200-151075200	Enhancers	Lung	lung
32	chr4:151074200-151075200	Enhancers	Ovary	ovary
33	chr4:151074200-151075400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr4:151074400-151074600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr4:151074400-151074800	Enhancers	Stomach Smooth Muscle	stomach
36	chr4:151074400-151081800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:151074400-151091800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:151074400-151094200	Weak transcription	NH-A	brain

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