Variant report

Variant	rs1868076
Chromosome Location	chr2:133554288-133554289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10187405	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1025388	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1025389	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1026076	0.88[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10928435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12616282	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12691829	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12691830	0.82[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13386826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13389587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1367391	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1447554	0.82[EUR][1000 genomes]
rs17325914	0.85[GIH][hapmap]
rs1839004	0.82[EUR][1000 genomes]
rs2166744	0.85[CHB][hapmap]
rs4953988	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4953989	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4953990	0.82[ASW][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap]
rs4953991	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953998	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs56318788	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6430374	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6430377	0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs6708285	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6729115	0.86[EUR][1000 genomes]
rs748487	0.80[EUR][1000 genomes]
rs7557503	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7568532	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7589873	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7592077	0.81[TSI][hapmap]
rs7601347	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7605691	0.82[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7606248	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs895715	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv875138	chr2:133410921-133761794	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1002955	chr2:133440142-133743211	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv834379	chr2:133471980-133665601	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1868076	LYPD1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133530800-133554400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:133531400-133561400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:133538200-133561200	Weak transcription	Hela-S3	cervix
4	chr2:133540400-133561800	Weak transcription	Brain Angular Gyrus	brain
5	chr2:133541000-133561200	Weak transcription	Brain Anterior Caudate	brain
6	chr2:133541200-133560800	Weak transcription	Fetal Brain Female	brain
7	chr2:133541800-133556600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:133542600-133561200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:133543000-133561800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:133543400-133561400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:133548000-133555800	Weak transcription	Ovary	ovary
12	chr2:133548400-133561200	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:133551000-133562000	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:133553000-133555200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:133553000-133558000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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