Variant report

Variant	rs2742552
Chromosome Location	chr11:8876852-8876853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10743093	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10769967	0.92[CEU][hapmap]
rs10769968	0.82[EUR][1000 genomes]
rs10769970	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs10769971	0.80[EUR][1000 genomes]
rs10769973	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs10769979	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs10840130	0.85[CEU][hapmap]
rs10840134	0.92[CEU][hapmap]
rs10840135	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs10840136	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840141	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840142	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840147	0.96[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs10840148	0.92[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11042078	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs11042102	0.83[EUR][1000 genomes]
rs11042103	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11042104	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs11042125	0.91[MEX][hapmap]
rs11042149	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs11042151	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs11042154	0.85[CEU][hapmap];0.83[MEX][hapmap]
rs1123936	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs11603841	0.96[CEU][hapmap]
rs1368017	0.95[JPT][hapmap]
rs1529641	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1560569	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs1569408	0.82[EUR][1000 genomes]
rs16906256	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs1883098	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1980428	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap]
rs1980429	0.92[CEU][hapmap]
rs1988708	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1988709	0.83[EUR][1000 genomes]
rs2016942	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs2568031	0.81[JPT][hapmap]
rs2568032	0.81[JPT][hapmap]
rs2568043	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2568045	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap]
rs2568054	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568059	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568061	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568062	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568065	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568090	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs2653567	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653570	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs2653593	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653605	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs2653607	0.86[ASN][1000 genomes]
rs2653613	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653616	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742480	0.92[CEU][hapmap]
rs2742536	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742537	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742550	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34842234	0.82[EUR][1000 genomes]
rs4909952	0.85[CEU][hapmap]
rs4910062	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4910157	0.86[EUR][1000 genomes]
rs4929922	0.87[MEX][hapmap]
rs7118463	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7119939	0.88[CEU][hapmap]
rs7123429	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7123861	0.81[EUR][1000 genomes]
rs7479407	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs7925728	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs7930026	0.84[CEU][hapmap]
rs7937298	0.92[CEU][hapmap]
rs7945705	0.92[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2742552	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs2742552	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2742552	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2742552	ST5	cis	parietal	SCAN
rs2742552	NRIP3	cis	parietal	SCAN
rs2742552	OR52A1	cis	parietal	SCAN
rs2742552	TUB	cis	parietal	SCAN
rs2742552	TMEM9B	cis	parietal	SCAN
rs2742552	RRP8	cis	parietal	SCAN
rs2742552	TMEM9B-AS1	cis	lung	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8862200-8881200	Weak transcription	Hela-S3	cervix
2	chr11:8862400-8880000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:8862400-8880000	Weak transcription	Spleen	Spleen
4	chr11:8862400-8885000	Weak transcription	NHLF	lung
5	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
6	chr11:8862600-8885200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine
9	chr11:8865800-8886000	Weak transcription	Fetal Stomach	stomach
10	chr11:8868800-8877000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:8871000-8877000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:8873200-8885000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:8874200-8880400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:8874600-8877000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:8874600-8885000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:8874800-8879000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:8874800-8880600	Weak transcription	Placenta	Placenta
18	chr11:8875000-8879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:8876200-8877400	Enhancers	Ovary	ovary
20	chr11:8876600-8877400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:8876800-8877000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:8876800-8877000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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