Variant report

Variant	rs2568068
Chromosome Location	chr11:8977830-8977831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8976504..8978770-chr11:8984640..8987251,2	K562	blood:
2	chr11:8977155..8979531-chr11:8982227..8985372,3	MCF-7	breast:
3	chr11:8968022..8970706-chr11:8976759..8978871,2	K562	blood:
4	chr11:8977298..8978907-chr11:8986024..8987853,3	K562	blood:

Variant related genes	Relation type
ENSG00000175348	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10279	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042114	0.82[EUR][1000 genomes]
rs11042115	0.81[EUR][1000 genomes]
rs11042116	0.81[EUR][1000 genomes]
rs11042127	0.91[EUR][1000 genomes]
rs11042133	0.91[EUR][1000 genomes]
rs1109304	0.91[EUR][1000 genomes]
rs12049908	0.82[EUR][1000 genomes]
rs2163626	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248245	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2568044	0.88[ASN][1000 genomes]
rs2568070	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568089	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568091	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568092	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2568094	0.90[ASN][1000 genomes]
rs2653569	0.86[ASN][1000 genomes]
rs2653573	0.90[ASN][1000 genomes]
rs2742478	0.89[ASN][1000 genomes]
rs2742484	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2742485	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3751064	0.91[EUR][1000 genomes]
rs3763913	0.87[EUR][1000 genomes]
rs3763914	0.87[EUR][1000 genomes]
rs56680262	0.91[EUR][1000 genomes]
rs72632952	0.81[EUR][1000 genomes]
rs7938995	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2568068	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs2568068	TMEM9B-AS1	cis	lung	GTEx
rs2568068	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2568068	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs2568068	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs2568068	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2568068	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs2568068	TMEM9B-AS1	cis	Thyroid	GTEx
rs2568068	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs2568068	TMEM9B-AS1	cis	Stomach	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8944600-8985000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:8954400-8984400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:8957000-8980800	Weak transcription	Fetal Heart	heart
4	chr11:8963200-8985000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:8965800-8984800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:8966400-8984000	Weak transcription	Fetal Brain Male	brain
7	chr11:8966800-8980800	Weak transcription	Small Intestine	intestine
8	chr11:8968000-8978200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:8968000-8978400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:8968200-8980800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:8968200-8985000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:8968400-8978600	Strong transcription	Liver	Liver
13	chr11:8968400-8979000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:8968400-8979200	Strong transcription	Primary B cells from cord blood	blood
15	chr11:8968600-8978000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:8968600-8978000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:8968600-8978800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr11:8968600-8978800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr11:8968600-8979400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:8968600-8981000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:8968800-8978000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:8968800-8978000	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr11:8968800-8978000	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:8968800-8978400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:8968800-8978400	Strong transcription	Fetal Intestine Large	intestine
26	chr11:8968800-8978600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:8968800-8978600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:8968800-8978600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:8968800-8978600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:8968800-8978800	Strong transcription	Fetal Muscle Leg	muscle
31	chr11:8968800-8978800	Strong transcription	Placenta	Placenta
32	chr11:8968800-8978800	Strong transcription	Left Ventricle	heart
33	chr11:8968800-8979200	Strong transcription	Adipose Nuclei	Adipose
34	chr11:8968800-8980800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr11:8969000-8978000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr11:8969000-8978000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:8969000-8978600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:8969000-8979200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr11:8969400-8978600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:8969400-8980800	Weak transcription	HSMMtube	muscle
41	chr11:8970200-8981000	Weak transcription	NHEK	skin
42	chr11:8970400-8978400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:8970600-8984400	Weak transcription	Right Ventricle	heart
44	chr11:8970600-8985000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr11:8970800-8980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr11:8970800-8984400	Weak transcription	A549	lung
47	chr11:8971000-8978800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:8971000-8980600	Weak transcription	Psoas Muscle	Psoas
49	chr11:8971200-8978600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:8971200-8984400	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links