Variant report

Variant	rs2568062
Chromosome Location	chr11:8887945-8887946
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	chr11:8885722..8888540-chr11:9189607..9191630,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10743093	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10743095	0.86[EUR][1000 genomes]
rs10769967	0.83[EUR][1000 genomes]
rs10769968	0.98[EUR][1000 genomes]
rs10769970	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10769971	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10769973	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840130	0.81[EUR][1000 genomes]
rs10840134	0.84[EUR][1000 genomes]
rs10840136	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840141	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840142	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10840147	0.96[EUR][1000 genomes]
rs10840148	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042078	0.81[EUR][1000 genomes]
rs11042079	0.81[EUR][1000 genomes]
rs11042082	0.83[EUR][1000 genomes]
rs11042088	0.83[EUR][1000 genomes]
rs11042102	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042103	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11042125	0.83[EUR][1000 genomes]
rs1109305	0.86[EUR][1000 genomes]
rs11603841	0.83[EUR][1000 genomes]
rs1529641	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1560569	0.86[EUR][1000 genomes]
rs1569408	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1883098	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988708	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988709	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2016942	0.86[EUR][1000 genomes]
rs2568043	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568054	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568059	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568061	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568065	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568090	0.83[EUR][1000 genomes]
rs2653567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653593	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653606	0.83[EUR][1000 genomes]
rs2653607	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653613	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653616	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742536	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2742537	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742540	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742545	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742550	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742552	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34842234	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36192694	0.84[EUR][1000 genomes]
rs4554887	0.83[EUR][1000 genomes]
rs4909952	0.83[EUR][1000 genomes]
rs4910062	0.84[EUR][1000 genomes]
rs4910119	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4910156	0.85[EUR][1000 genomes]
rs4910158	0.85[EUR][1000 genomes]
rs4910200	0.84[EUR][1000 genomes]
rs61876187	0.83[EUR][1000 genomes]
rs7118463	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7119939	0.84[EUR][1000 genomes]
rs7123429	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7123861	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7937298	0.92[EUR][1000 genomes]
rs7943377	0.82[EUR][1000 genomes]
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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2568062	TMEM9B-AS1	cis	lung	GTEx
rs2568062	AKIP1	cis	Thyroid	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
2	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine
4	chr11:8877400-8888600	Weak transcription	Fetal Muscle Leg	muscle
5	chr11:8877400-8888600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:8878200-8891800	Weak transcription	Psoas Muscle	Psoas
7	chr11:8880200-8892000	Weak transcription	Gastric	stomach
8	chr11:8880400-8888000	Weak transcription	Stomach Mucosa	stomach
9	chr11:8880400-8888200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:8880400-8889200	Weak transcription	Lung	lung
11	chr11:8881400-8888200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:8884200-8889600	Enhancers	NHDF-Ad	bronchial
13	chr11:8884400-8889000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:8884400-8891800	Weak transcription	Left Ventricle	heart
15	chr11:8885000-8888200	Enhancers	NHLF	lung
16	chr11:8885200-8889000	Enhancers	HUVEC	blood vessel
17	chr11:8885600-8888000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:8885600-8891400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:8885600-8891400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:8885800-8888000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:8885800-8888400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:8885800-8888400	Weak transcription	A549	lung
23	chr11:8885800-8889600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:8885800-8889800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:8885800-8889800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:8885800-8891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:8885800-8891400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:8885800-8891400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:8885800-8891800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:8886000-8888000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:8886000-8888000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:8886000-8888200	Weak transcription	Small Intestine	intestine
33	chr11:8886000-8888200	Weak transcription	HSMM	muscle
34	chr11:8886000-8889400	Weak transcription	HSMMtube	muscle
35	chr11:8886000-8889600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:8886000-8889600	Weak transcription	Ovary	ovary
37	chr11:8886200-8888000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:8886200-8888000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr11:8886200-8888000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:8886200-8888000	Weak transcription	Placenta	Placenta
41	chr11:8886200-8888000	Weak transcription	NH-A	brain
42	chr11:8886200-8889600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:8886200-8889600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:8886400-8888200	Weak transcription	Osteobl	bone
45	chr11:8886600-8888000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:8886600-8888200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:8886600-8888400	Weak transcription	Fetal Stomach	stomach
48	chr11:8886800-8889600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:8887000-8890200	Enhancers	Fetal Lung	lung
50	chr11:8887200-8888000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links