Variant report

Variant	rs2742545
Chromosome Location	chr11:8884308-8884309
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10743093	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs10769958	0.81[CEU][hapmap]
rs10769967	0.93[CEU][hapmap]
rs10769968	0.82[EUR][1000 genomes]
rs10769970	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs10769971	0.80[EUR][1000 genomes]
rs10769973	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs10769979	0.85[CEU][hapmap]
rs10840130	0.85[CEU][hapmap]
rs10840134	0.92[CEU][hapmap]
rs10840135	0.95[JPT][hapmap]
rs10840136	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840141	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840142	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10840147	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs10840148	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs11042078	0.89[CEU][hapmap]
rs11042102	0.83[EUR][1000 genomes]
rs11042103	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs11042104	0.95[JPT][hapmap]
rs11042149	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11042151	0.85[CEU][hapmap]
rs11042154	0.85[CEU][hapmap]
rs1123936	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11603841	0.96[CEU][hapmap]
rs12224436	0.81[CEU][hapmap]
rs12421789	0.81[CEU][hapmap]
rs1368017	0.91[JPT][hapmap]
rs1529641	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs1560569	0.85[CEU][hapmap]
rs1569408	0.82[EUR][1000 genomes]
rs16906256	0.95[JPT][hapmap]
rs1883098	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980428	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1980429	0.92[CEU][hapmap]
rs1988708	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988709	0.83[EUR][1000 genomes]
rs2016942	0.85[CEU][hapmap]
rs2568031	0.81[JPT][hapmap]
rs2568032	0.81[JPT][hapmap]
rs2568043	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2568045	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2568054	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568059	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568061	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568062	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568090	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs2653567	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653570	0.89[CEU][hapmap]
rs2653593	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653605	0.92[CEU][hapmap]
rs2653607	0.84[ASN][1000 genomes]
rs2653613	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653616	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742480	0.93[CEU][hapmap]
rs2742536	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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];0.98[ASN][1000 genomes]
rs2742540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742550	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742552	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]
rs34842234	0.82[EUR][1000 genomes]
rs4579928	0.81[CEU][hapmap]
rs4909952	0.85[CEU][hapmap]
rs4910062	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4910157	0.86[EUR][1000 genomes]
rs4929916	0.81[CEU][hapmap]
rs6484484	0.81[CEU][hapmap]
rs6486060	0.81[CEU][hapmap]
rs7118463	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7119939	0.88[CEU][hapmap]
rs7123429	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7123861	0.81[EUR][1000 genomes]
rs7479407	0.85[CEU][hapmap]
rs7925728	0.85[CEU][hapmap]
rs7930026	0.85[CEU][hapmap]
rs7937298	0.93[CEU][hapmap]
rs7944560	0.81[CEU][hapmap]
rs7945705	0.92[CEU][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2742545	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2742545	TMEM9B-AS1	cis	lung	GTEx
rs2742545	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2742545	TMEM9B-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8862400-8885000	Weak transcription	NHLF	lung
2	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
3	chr11:8862600-8885200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine
6	chr11:8865800-8886000	Weak transcription	Fetal Stomach	stomach
7	chr11:8873200-8885000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:8874600-8885000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:8877400-8888600	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:8877400-8888600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:8878200-8891800	Weak transcription	Psoas Muscle	Psoas
12	chr11:8879400-8885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:8880200-8892000	Weak transcription	Gastric	stomach
14	chr11:8880400-8885800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:8880400-8888000	Weak transcription	Stomach Mucosa	stomach
16	chr11:8880400-8888200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:8880400-8889200	Weak transcription	Lung	lung
18	chr11:8880600-8885000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:8880800-8885000	Weak transcription	Placenta	Placenta
20	chr11:8881400-8888200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:8881600-8885000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:8881600-8885000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:8881800-8884400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:8882000-8884400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:8882200-8885000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:8883200-8885400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:8884000-8884400	Enhancers	Left Ventricle	heart
28	chr11:8884000-8884400	Enhancers	Ovary	ovary
29	chr11:8884000-8884600	Enhancers	Spleen	Spleen
30	chr11:8884000-8884800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:8884200-8884400	Enhancers	Small Intestine	intestine
32	chr11:8884200-8887200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:8884200-8887200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:8884200-8887800	Enhancers	Hela-S3	cervix
35	chr11:8884200-8889600	Enhancers	NHDF-Ad	bronchial

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