Variant report

Variant	rs1368017
Chromosome Location	chr11:8867070-8867071
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10743091	0.86[EUR][1000 genomes]
rs10840135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840137	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042097	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042098	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042104	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1123936	0.83[JPT][hapmap]
rs12049908	0.84[YRI][hapmap]
rs12798322	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16906256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1980428	0.83[JPT][hapmap]
rs2292049	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2568031	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2568032	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2568045	0.83[JPT][hapmap]
rs2568061	0.95[JPT][hapmap]
rs2568065	0.95[JPT][hapmap]
rs2742536	0.95[JPT][hapmap]
rs2742537	0.91[JPT][hapmap]
rs2742540	0.95[JPT][hapmap]
rs2742545	0.91[JPT][hapmap]
rs2742552	0.95[JPT][hapmap]
rs34874636	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59025804	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61876202	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7123429	0.96[JPT][hapmap]
rs7127479	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7948452	0.87[AMR][1000 genomes];0.94[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	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1368017	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1368017	TMEM9B-AS1	cis	Stomach	GTEx
rs1368017	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs1368017	TMEM9B	Cis_1M	lymphoblastoid	RTeQTL
rs1368017	TMEM9B-AS1	cis	lung	GTEx
rs1368017	TMEM9B-AS1	cis	Thyroid	GTEx
rs1368017	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs1368017	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8862200-8881200	Weak transcription	Hela-S3	cervix
2	chr11:8862400-8867800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:8862400-8867800	Weak transcription	Ovary	ovary
4	chr11:8862400-8868000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:8862400-8868000	Weak transcription	Left Ventricle	heart
6	chr11:8862400-8870600	Weak transcription	Placenta	Placenta
7	chr11:8862400-8874600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:8862400-8880000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:8862400-8880000	Weak transcription	Spleen	Spleen
10	chr11:8862400-8885000	Weak transcription	NHLF	lung
11	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
12	chr11:8862600-8867800	Weak transcription	Brain Substantia Nigra	brain
13	chr11:8862600-8868400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:8862600-8868800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:8862600-8876600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:8862600-8885200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr11:8863200-8867200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr11:8864000-8872200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine
21	chr11:8865400-8867600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:8865400-8873600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:8865600-8867600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:8865800-8867600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr11:8865800-8886000	Weak transcription	Fetal Stomach	stomach
26	chr11:8866000-8874200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:8866400-8867400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:8867000-8867400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr11:8867000-8867600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:8867000-8867800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:8867000-8867800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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