Variant report

Variant	rs10840130
Chromosome Location	chr11:8830801-8830802
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8708349..8711473-chr11:8829326..8831114,3	K562	blood:
2	chr11:8706888..8711251-chr11:8829326..8831400,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM66-7	chr11:8829373-8832882	NONHSAT017885

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction
ENSG00000212607	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10743093	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10769948	0.80[AMR][1000 genomes]
rs10769955	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10769957	1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10769967	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10769968	0.80[EUR][1000 genomes]
rs10769970	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs10769973	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs10769979	0.84[CEU][hapmap]
rs10840114	1.00[YRI][hapmap]
rs10840134	0.92[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10840141	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs10840142	0.92[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs10840147	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs10840148	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs11042059	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs11042060	0.82[AMR][1000 genomes]
rs11042069	1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11042078	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042079	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042082	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042088	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042102	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11042103	0.92[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs11042151	0.84[CEU][hapmap]
rs11042154	0.84[CEU][hapmap]
rs11603841	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12224436	0.82[AMR][1000 genomes]
rs12794444	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529641	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs1560569	0.84[CEU][hapmap]
rs1569408	0.80[EUR][1000 genomes]
rs1883098	0.81[EUR][1000 genomes]
rs1980429	0.82[JPT][hapmap]
rs1988708	0.81[EUR][1000 genomes]
rs1988709	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2016942	0.84[CEU][hapmap]
rs2316865	1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2568043	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs2568054	0.81[EUR][1000 genomes]
rs2568059	0.82[EUR][1000 genomes]
rs2568061	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2568062	0.81[EUR][1000 genomes]
rs2568065	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2568090	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2653567	0.81[EUR][1000 genomes]
rs2653593	0.81[EUR][1000 genomes]
rs2653606	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2653607	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2653616	0.82[EUR][1000 genomes]
rs2742540	0.84[CEU][hapmap]
rs2742545	0.85[CEU][hapmap]
rs2742550	0.82[EUR][1000 genomes]
rs2742552	0.85[CEU][hapmap]
rs34842234	0.81[EUR][1000 genomes]
rs4554887	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4909952	0.88[CEU][hapmap]
rs4910062	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4929911	0.82[AMR][1000 genomes]
rs4929912	0.81[AMR][1000 genomes]
rs4929914	0.84[CHB][hapmap];0.81[AMR][1000 genomes]
rs4929916	0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs61876187	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7119939	0.88[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7123429	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7123861	0.82[EUR][1000 genomes]
rs7479407	0.84[CEU][hapmap]
rs7925728	0.84[CEU][hapmap]
rs7930026	0.84[CEU][hapmap]
rs7937298	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7940366	1.00[YRI][hapmap]
rs7943377	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7945705	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs905290	1.00[YRI][hapmap]
rs978636	0.91[AMR][1000 genomes];0.98[EUR][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	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527073	chr11:8829168-8848463	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840130	TMEM9B-AS1	cis	lung	GTEx
rs10840130	AKIP1	cis	Thyroid	GTEx
rs10840130	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8816400-8831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:8827400-8831200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:8827600-8831000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr11:8828200-8831000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:8828400-8831000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:8828600-8831000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr11:8828600-8831200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:8828600-8831200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:8828600-8831200	Flanking Active TSS	HSMMtube	muscle
10	chr11:8828600-8831200	Flanking Active TSS	NHEK	skin
11	chr11:8828600-8831400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr11:8828600-8831400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr11:8828800-8831000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:8828800-8831600	Enhancers	Fetal Thymus	thymus
15	chr11:8828800-8831600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr11:8828800-8833200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:8829000-8831200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:8829000-8831400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:8829000-8831600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:8829000-8832200	Flanking Active TSS	Osteobl	bone
21	chr11:8829000-8832800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr11:8829200-8831400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:8829400-8831200	Flanking Active TSS	NHLF	lung
24	chr11:8829400-8831400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:8829400-8832000	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr11:8829400-8832800	Genic enhancers	Placenta	Placenta
27	chr11:8829400-8833000	Flanking Active TSS	NH-A	brain
28	chr11:8829600-8831000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr11:8829600-8831000	Enhancers	HepG2	liver
30	chr11:8829600-8831200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr11:8829600-8831400	Weak transcription	Liver	Liver
32	chr11:8830000-8832600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr11:8830000-8832600	Active TSS	Right Atrium	heart
34	chr11:8830200-8831200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:8830200-8831200	Active TSS	Fetal Brain Male	brain
36	chr11:8830200-8831400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:8830200-8831800	Weak transcription	Spleen	Spleen
38	chr11:8830200-8831800	Flanking Active TSS	Hela-S3	cervix
39	chr11:8830200-8832800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:8830200-8833000	Active TSS	Colon Smooth Muscle	Colon
41	chr11:8830400-8831000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:8830400-8831200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr11:8830400-8831200	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr11:8830400-8831200	Flanking Active TSS	Psoas Muscle	Psoas
45	chr11:8830400-8831200	Flanking Active TSS	NHDF-Ad	bronchial
46	chr11:8830400-8831400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr11:8830400-8831400	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr11:8830400-8831600	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr11:8830400-8831600	Active TSS	Fetal Brain Female	brain
50	chr11:8830400-8832600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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