Variant report

Variant	rs10769967
Chromosome Location	chr11:8858730-8858731
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	chr11:8856465..8859459-chr11:8859495..8861215,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10743093	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10769947	0.81[CEU][hapmap]
rs10769948	0.81[CEU][hapmap]
rs10769957	0.81[CEU][hapmap]
rs10769968	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10769970	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10769971	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10769973	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10769979	0.93[CEU][hapmap]
rs10840130	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]
rs10840134	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840141	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10840142	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840147	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10840148	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11042078	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042079	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042082	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042088	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11042102	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042103	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]
rs11042125	0.82[JPT][hapmap]
rs11042149	0.81[CEU][hapmap]
rs11042151	0.93[CEU][hapmap]
rs11042154	0.93[CEU][hapmap]
rs1123936	0.85[CEU][hapmap]
rs11603841	0.96[CEU][hapmap];0.80[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12224436	0.82[CEU][hapmap]
rs12794444	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1529641	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1560569	0.93[CEU][hapmap]
rs1569408	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1883098	0.82[EUR][1000 genomes]
rs1980428	0.85[CEU][hapmap]
rs1980429	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs1988708	0.82[EUR][1000 genomes]
rs1988709	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2016942	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs2568043	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568045	0.85[CEU][hapmap]
rs2568054	0.82[EUR][1000 genomes]
rs2568059	0.84[EUR][1000 genomes]
rs2568061	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2568062	0.83[EUR][1000 genomes]
rs2568065	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2568090	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2653567	0.82[EUR][1000 genomes]
rs2653570	0.81[CEU][hapmap]
rs2653593	0.84[EUR][1000 genomes]
rs2653605	0.85[CEU][hapmap]
rs2653606	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2653607	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2653616	0.83[EUR][1000 genomes]
rs2742480	0.85[CEU][hapmap]
rs2742536	0.82[CEU][hapmap]
rs2742537	0.88[CEU][hapmap]
rs2742540	0.92[CEU][hapmap]
rs2742545	0.93[CEU][hapmap]
rs2742550	0.83[EUR][1000 genomes]
rs2742552	0.92[CEU][hapmap]
rs34842234	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4554887	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4909952	0.93[CEU][hapmap];0.81[JPT][hapmap]
rs4910062	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910119	0.82[AMR][1000 genomes]
rs4910442	0.81[CEU][hapmap]
rs4929911	0.81[CEU][hapmap]
rs4929912	0.81[CEU][hapmap]
rs4929914	0.81[CEU][hapmap]
rs4929922	0.82[JPT][hapmap]
rs61876187	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6486060	0.85[CEU][hapmap]
rs7119939	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7123429	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7123861	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7479407	0.93[CEU][hapmap]
rs7925728	0.93[CEU][hapmap]
rs7930026	0.92[CEU][hapmap]
rs7937298	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7943377	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7945705	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7947631	0.83[CEU][hapmap]
rs905290	0.80[CEU][hapmap]
rs978636	0.84[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10769967	TMEM9B-AS1	cis	lung	GTEx
rs10769967	AKIP1	cis	Thyroid	GTEx
rs10769967	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8833200-8859800	Weak transcription	Aorta	Aorta
2	chr11:8845800-8860000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr11:8851000-8859200	Weak transcription	Fetal Lung	lung
4	chr11:8851000-8861400	Weak transcription	Brain Substantia Nigra	brain
5	chr11:8851800-8862400	Enhancers	Placenta	Placenta
6	chr11:8852000-8859200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr11:8852800-8861600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:8853000-8861400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:8854400-8861000	Weak transcription	Pancreas	Pancrea
10	chr11:8854600-8859400	Weak transcription	Right Atrium	heart
11	chr11:8854600-8859400	Weak transcription	Stomach Mucosa	stomach
12	chr11:8854600-8860000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:8854600-8860400	Weak transcription	Gastric	stomach
14	chr11:8854600-8861000	Weak transcription	Lung	lung
15	chr11:8854600-8861400	Weak transcription	A549	lung
16	chr11:8854800-8859200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:8854800-8859400	Weak transcription	Ovary	ovary
18	chr11:8854800-8860600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:8854800-8861000	Weak transcription	Fetal Intestine Small	intestine
20	chr11:8855200-8859800	Weak transcription	Fetal Kidney	kidney
21	chr11:8855400-8859600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:8855400-8859800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:8855400-8861000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:8855400-8861000	Weak transcription	Esophagus	oesophagus
25	chr11:8855400-8861000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:8855400-8861800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:8855600-8859400	Weak transcription	Left Ventricle	heart
28	chr11:8855600-8859600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:8855600-8859800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:8855600-8859800	Weak transcription	Fetal Heart	heart
31	chr11:8855600-8860000	Weak transcription	Right Ventricle	heart
32	chr11:8855600-8861200	Weak transcription	Hela-S3	cervix
33	chr11:8855800-8859400	Weak transcription	Spleen	Spleen
34	chr11:8855800-8859800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:8855800-8859800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr11:8855800-8861200	Weak transcription	GM12878-XiMat	blood
37	chr11:8855800-8861600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:8856000-8859200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:8856000-8859200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:8856000-8859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr11:8856000-8859800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:8856000-8860000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr11:8856200-8859400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:8856200-8859400	Weak transcription	HMEC	breast
45	chr11:8856200-8859800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr11:8856200-8859800	Weak transcription	Colon Smooth Muscle	Colon
47	chr11:8856200-8860000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:8856200-8860200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:8856200-8860600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr11:8856200-8861200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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