Variant report

Variant	rs6692738
Chromosome Location	chr1:150166773-150166774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150158453..150162673-chr1:150163333..150168341,4	K562	blood:
2	chr1:149857548..149860200-chr1:150165414..150168428,4	K562	blood:

Variant related genes	Relation type
ENSG00000178096	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000184678	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10788872	0.84[ASN][1000 genomes]
rs10888574	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888576	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11205339	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205340	0.99[ASN][1000 genomes]
rs11205341	0.91[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs11205343	0.94[ASN][1000 genomes]
rs11205347	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11205348	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11811787	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12131063	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133235	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12133238	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136311	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12569047	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1535873	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924549	0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2038752	0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2038753	0.94[ASN][1000 genomes]
rs3118124	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121000	0.94[ASN][1000 genomes]
rs3121001	0.99[ASN][1000 genomes]
rs4408187	0.99[ASN][1000 genomes]
rs55647200	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55956539	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59507173	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61161619	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587753	0.94[ASN][1000 genomes]
rs6655935	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs6660127	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665499	0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6680040	0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6682434	0.98[ASN][1000 genomes]
rs6694215	0.94[ASN][1000 genomes]
rs6703332	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522034	0.82[GIH][hapmap];0.91[JPT][hapmap]
rs7532164	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535712	0.94[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7548543	0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7550600	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7551023	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555995	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv535153	chr1:150147218-150168829	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6692738	TNFAIP8L2	cis	cerebellum	SCAN
rs6692738	MRPS21	cis	parietal	SCAN
rs6692738	MRPS21	cis	cerebellum	SCAN
rs6692738	CGN	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150164200-150166800	Enhancers	NH-A	brain
2	chr1:150165000-150166800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:150165000-150166800	Weak transcription	NHLF	lung
4	chr1:150165200-150166800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:150165600-150166800	Weak transcription	A549	lung
6	chr1:150165800-150166800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:150165800-150166800	Weak transcription	HSMM	muscle
8	chr1:150166000-150167000	Weak transcription	Fetal Heart	heart
9	chr1:150166400-150166800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:150166400-150166800	Enhancers	Osteobl	bone
11	chr1:150166600-150167000	Enhancers	K562	blood
12	chr1:150166600-150167200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:150166600-150167400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:150166600-150167400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:150166600-150167400	Enhancers	NHDF-Ad	bronchial
16	chr1:150166600-150167600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:150166600-150167600	Enhancers	HSMMtube	muscle

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