Variant report

Variant	rs11042059
Chromosome Location	chr11:8795080-8795081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8714620..8716803-chr11:8793970..8795486,2	K562	blood:
2	chr11:8792754..8796675-chr11:8797137..8799307,3	K562	blood:

Variant related genes	Relation type
ENSG00000254665	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10769947	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769948	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769958	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10840114	1.00[YRI][hapmap]
rs10840130	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs10840134	0.81[CEU][hapmap]
rs10840148	0.81[CEU][hapmap]
rs11042055	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042067	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042079	0.81[AMR][1000 genomes]
rs11042082	0.80[AMR][1000 genomes]
rs12224436	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12421789	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2316865	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568061	0.81[CEU][hapmap]
rs2568065	0.81[CEU][hapmap]
rs2568090	0.81[CEU][hapmap]
rs3763918	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3794153	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4554887	0.80[AMR][1000 genomes]
rs4579928	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4910062	1.00[YRI][hapmap]
rs4929911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4929912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4929914	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4929916	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61876187	0.81[AMR][1000 genomes]
rs6484484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6484496	0.86[EUR][1000 genomes]
rs7107867	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7129667	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7940366	1.00[YRI][hapmap]
rs7944560	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7945705	0.81[CEU][hapmap]
rs905290	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11042059	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs11042059	TMEM9B-AS1	cis	lung	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8777400-8795800	Enhancers	Rectal Smooth Muscle	rectum
2	chr11:8779600-8799600	Weak transcription	Fetal Brain Male	brain
3	chr11:8785200-8799400	Enhancers	Fetal Heart	heart
4	chr11:8786600-8795400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:8786600-8795400	Enhancers	Stomach Mucosa	stomach
6	chr11:8786600-8798000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:8786600-8803000	Enhancers	Ovary	ovary
8	chr11:8787000-8797800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:8788200-8797000	Weak transcription	Brain Hippocampus Middle	brain
10	chr11:8788600-8799600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:8788800-8801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:8788800-8808400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:8789000-8795400	Enhancers	HMEC	breast
14	chr11:8789000-8801200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:8789400-8797000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:8789400-8797400	Weak transcription	Brain Substantia Nigra	brain
17	chr11:8789400-8807600	Weak transcription	Fetal Kidney	kidney
18	chr11:8789600-8799400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:8789600-8805800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:8790400-8795600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr11:8790400-8795800	Weak transcription	Small Intestine	intestine
22	chr11:8790600-8796000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:8790800-8797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:8791400-8795600	Weak transcription	Fetal Thymus	thymus
25	chr11:8791400-8797000	Weak transcription	Psoas Muscle	Psoas
26	chr11:8791400-8810400	Weak transcription	Hela-S3	cervix
27	chr11:8791600-8796200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:8792200-8795400	Enhancers	NHDF-Ad	bronchial
29	chr11:8792200-8795600	Enhancers	NHEK	skin
30	chr11:8792400-8795200	Enhancers	Osteobl	bone
31	chr11:8792400-8795400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr11:8792400-8795600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:8792400-8795600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:8792400-8795800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
35	chr11:8792400-8796000	Genic enhancers	HSMM	muscle
36	chr11:8792400-8796400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:8792400-8797000	Enhancers	Colon Smooth Muscle	Colon
38	chr11:8792600-8795200	Enhancers	NH-A	brain
39	chr11:8792600-8802400	Genic enhancers	Fetal Stomach	stomach
40	chr11:8792800-8795200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:8793000-8797600	Enhancers	NHLF	lung
42	chr11:8793000-8798000	Weak transcription	Liver	Liver
43	chr11:8793200-8801600	Genic enhancers	Fetal Muscle Leg	muscle
44	chr11:8793800-8795200	Enhancers	Placenta	Placenta
45	chr11:8794000-8795200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr11:8794000-8796800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:8794000-8799400	Enhancers	Spleen	Spleen
48	chr11:8794200-8795200	Genic enhancers	Fetal Intestine Small	intestine
49	chr11:8794200-8795400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:8794200-8795400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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