Variant report

Variant	rs2742480
Chromosome Location	chr11:8993130-8993131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8985985..8989879-chr11:8990022..8995135,9	K562	blood:
2	chr11:8708369..8710243-chr11:8992642..8995400,2	K562	blood:
3	chr11:8991559..8993834-chr11:9003227..9005288,2	MCF-7	breast:
4	chr11:8992414..8994914-chr11:9017191..9020958,3	K562	blood:
5	chr11:8984840..8989436-chr11:8990874..8994927,8	MCF-7	breast:
6	chr11:8983613..8986337-chr11:8992669..8994467,2	MCF-7	breast:
7	chr11:8992487..8994704-chr11:9009691..9012434,3	K562	blood:

Variant related genes	Relation type
ENSG00000254860	Chromatin interaction
ENSG00000175348	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10743093	0.85[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap]
rs10769967	0.85[CEU][hapmap]
rs10769970	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10769971	0.88[JPT][hapmap]
rs10769973	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs10769979	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10769980	0.98[ASN][1000 genomes]
rs10769981	0.84[ASN][1000 genomes]
rs10840134	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10840136	0.80[EUR][1000 genomes]
rs10840141	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10840142	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10840147	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840148	0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840157	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840158	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042078	0.80[CEU][hapmap]
rs11042103	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11042125	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11042149	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042150	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042151	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11042152	0.98[ASN][1000 genomes]
rs11042154	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1109305	0.82[ASN][1000 genomes]
rs1123936	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11603841	0.88[CEU][hapmap]
rs1529641	0.83[CEU][hapmap]
rs1560569	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1980428	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1980429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1984791	0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2012680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012690	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012696	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016942	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2455603	0.86[YRI][hapmap]
rs2568020	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568021	0.93[YRI][hapmap]
rs2568027	0.80[YRI][hapmap]
rs2568043	0.85[CEU][hapmap]
rs2568045	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568061	0.84[CEU][hapmap]
rs2568065	0.84[CEU][hapmap]
rs2568090	0.84[CEU][hapmap]
rs2653570	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653588	0.82[YRI][hapmap]
rs2653605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742470	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742471	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742474	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742479	0.89[YRI][hapmap]
rs2742518	0.81[YRI][hapmap]
rs2742536	0.82[CEU][hapmap]
rs2742537	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2742540	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2742545	0.93[CEU][hapmap]
rs2742552	0.92[CEU][hapmap]
rs4909952	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4910062	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs4910156	0.80[ASN][1000 genomes]
rs4910157	0.87[EUR][1000 genomes]
rs4910200	0.86[ASN][1000 genomes]
rs4910442	0.81[CEU][hapmap]
rs4929922	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6486060	0.85[CEU][hapmap]
rs7118463	0.82[EUR][1000 genomes]
rs7119939	0.84[CEU][hapmap]
rs7123429	0.85[CEU][hapmap]
rs7479407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7482838	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7484180	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925728	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7930026	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs7937298	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs7945705	0.84[CEU][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2742480	TMEM9B-AS1	cis	lung	GTEx
rs2742480	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2742480	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs2742480	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs2742480	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs2742480	TMEM9B-AS1	cis	Thyroid	GTEx
rs2742480	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2742480	TMEM9B-AS1	cis	Stomach	GTEx
rs2742480	TMEM9B-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8986800-8993600	Weak transcription	Aorta	Aorta
2	chr11:8986800-8994400	Weak transcription	Ovary	ovary
3	chr11:8986800-8995000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:8986800-8996600	Weak transcription	Spleen	Spleen
5	chr11:8987000-8993600	Weak transcription	Left Ventricle	heart
6	chr11:8987000-8994200	Weak transcription	Psoas Muscle	Psoas
7	chr11:8987000-8994800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:8987000-8995000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:8987000-9007200	Weak transcription	Brain Germinal Matrix	brain
10	chr11:8987000-9007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:8987000-9010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:8987000-9011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:8987200-8993800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:8987600-8993400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:8987600-9005000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:8987600-9006400	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:8987600-9010000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:8987600-9010000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:8987800-8993200	Weak transcription	Liver	Liver
20	chr11:8987800-8993200	Weak transcription	Right Ventricle	heart
21	chr11:8987800-8994400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr11:8987800-8994400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr11:8987800-8999000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:8987800-9005000	Weak transcription	Brain Angular Gyrus	brain
25	chr11:8987800-9010200	Weak transcription	NHDF-Ad	bronchial
26	chr11:8987800-9012000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:8989200-8999000	Weak transcription	Fetal Intestine Small	intestine
28	chr11:8989600-8994600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:8989600-8997000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:8989600-8997400	Weak transcription	Primary T cells from cord blood	blood
31	chr11:8989600-9001400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:8989600-9002400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr11:8989600-9003400	Weak transcription	Fetal Stomach	stomach
34	chr11:8989600-9010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:8989600-9011200	Weak transcription	Brain Anterior Caudate	brain
36	chr11:8989600-9019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:8991800-9015600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:8992400-8999200	Weak transcription	Placenta	Placenta
39	chr11:8992600-8993200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:8992800-8994000	Enhancers	K562	blood

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