Variant report

Variant	rs11042103
Chromosome Location	chr11:8888700-8888701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10743093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743095	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10769947	0.81[CEU][hapmap]
rs10769948	0.81[CEU][hapmap]
rs10769957	0.81[CEU][hapmap]
rs10769967	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10769968	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769971	0.86[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769973	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769979	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840130	0.92[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs10840134	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10840136	0.82[EUR][1000 genomes]
rs10840141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840147	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042078	0.96[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs11042079	0.81[EUR][1000 genomes]
rs11042082	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042088	0.83[EUR][1000 genomes]
rs11042102	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042125	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042149	0.81[CEU][hapmap]
rs11042151	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11042154	0.93[CEU][hapmap];0.80[JPT][hapmap]
rs1109305	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1123936	0.85[CEU][hapmap]
rs11603841	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12224436	0.82[CEU][hapmap]
rs1529641	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1560569	0.93[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1569408	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1883098	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1980428	0.85[CEU][hapmap]
rs1980429	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1984791	0.80[JPT][hapmap]
rs1988708	0.96[EUR][1000 genomes]
rs1988709	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016942	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2568043	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2568045	0.85[CEU][hapmap]
rs2568054	0.96[EUR][1000 genomes]
rs2568059	0.98[EUR][1000 genomes]
rs2568061	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2568062	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2568065	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568090	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2653567	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2653570	0.81[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2653593	0.97[EUR][1000 genomes]
rs2653605	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2653606	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2653607	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2653613	0.82[EUR][1000 genomes]
rs2653616	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2742480	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2742536	0.82[CEU][hapmap]
rs2742537	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2742540	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2742545	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2742550	0.97[EUR][1000 genomes]
rs2742552	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs34842234	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36192694	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4554887	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4909952	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910062	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4910119	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910156	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910157	0.86[ASN][1000 genomes]
rs4910158	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910200	0.84[EUR][1000 genomes]
rs4910442	0.81[CEU][hapmap]
rs4929911	0.81[CEU][hapmap]
rs4929912	0.81[CEU][hapmap]
rs4929914	0.81[CEU][hapmap]
rs4929922	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs61876187	0.83[EUR][1000 genomes]
rs6486060	0.85[CEU][hapmap]
rs7118463	0.80[EUR][1000 genomes]
rs7119939	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7123429	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7123861	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7479407	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7925728	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7930026	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs7937298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7943377	0.82[EUR][1000 genomes]
rs7945705	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7947631	0.83[CEU][hapmap]
rs905290	0.80[CEU][hapmap]
rs978636	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	esv3402630	chr11:8887304-8893757	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3325077	chr11:8887314-8893755	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11042103	TMEM9B-AS1	cis	lung	GTEx
rs11042103	AKIP1	cis	Thyroid	GTEx
rs11042103	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:8878200-8891800	Weak transcription	Psoas Muscle	Psoas
3	chr11:8880200-8892000	Weak transcription	Gastric	stomach
4	chr11:8880400-8889200	Weak transcription	Lung	lung
5	chr11:8884200-8889600	Enhancers	NHDF-Ad	bronchial
6	chr11:8884400-8889000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:8884400-8891800	Weak transcription	Left Ventricle	heart
8	chr11:8885200-8889000	Enhancers	HUVEC	blood vessel
9	chr11:8885600-8891400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:8885600-8891400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:8885800-8889600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:8885800-8889800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:8885800-8889800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:8885800-8891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:8885800-8891400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:8885800-8891400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr11:8885800-8891800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:8886000-8889400	Weak transcription	HSMMtube	muscle
19	chr11:8886000-8889600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:8886000-8889600	Weak transcription	Ovary	ovary
21	chr11:8886200-8889600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:8886200-8889600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:8886800-8889600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:8887000-8890200	Enhancers	Fetal Lung	lung
25	chr11:8887200-8891400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:8887200-8891600	Weak transcription	Adipose Nuclei	Adipose
27	chr11:8887200-8891800	Weak transcription	Brain Substantia Nigra	brain
28	chr11:8887200-8892000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:8887400-8889400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:8887400-8891400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:8887800-8889000	Flanking Active TSS	Hela-S3	cervix
32	chr11:8888000-8888800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:8888000-8889000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:8888000-8889200	Enhancers	Fetal Intestine Small	intestine
35	chr11:8888000-8889600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr11:8888000-8889800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:8888000-8890200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:8888000-8890400	Enhancers	NH-A	brain
39	chr11:8888000-8890600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:8888000-8890800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:8888000-8891600	Enhancers	Placenta	Placenta
42	chr11:8888000-8891600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr11:8888200-8888800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:8888200-8888800	Enhancers	Colonic Mucosa	Colon
45	chr11:8888200-8888800	Enhancers	Duodenum Mucosa	Duodenum
46	chr11:8888200-8888800	Enhancers	HSMM	muscle
47	chr11:8888200-8889000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:8888200-8889000	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr11:8888200-8889000	Enhancers	HMEC	breast
50	chr11:8888200-8889200	Enhancers	Fetal Intestine Large	intestine

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