Variant report

Variant	rs10279
Chromosome Location	chr11:8969309-8969310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr11:8969157-8969419	HepG2	liver:	n/a	n/a
2	MAFK	chr11:8968928-8969421	IMR90	lung:	n/a	chr11:8969006-8969021
3	CEBPB	chr11:8969028-8969378	IMR90	lung:	n/a	n/a
4	MAFK	chr11:8968956-8969310	HepG2	liver:	n/a	chr11:8969006-8969021

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:8969269-8969319	A549	lung:	n/a
2	chr11:8969269-8969319	HL-60	blood:	n/a
3	chr11:8969269-8969319	NT2-D1	testis:	n/a
4	chr11:8969269-8969319	ProgFib	skin:	n/a
5	chr11:8969269-8969319	ovcar-3	ovarian:	n/a
6	chr11:8969269-8969319	SK-N-SH_RA	brain:	n/a
7	chr11:8969269-8969319	HMEC	breast:	n/a
8	chr11:8969269-8969319	Caco-2	colon:	n/a
9	chr11:8969269-8969319	NH-A	brain:	n/a
10	chr11:8969269-8969319	HNPCEpiC	eye:	n/a
11	chr11:8969269-8969319	HEK293	kidney:	embryo
12	chr11:8969269-8969319	HIPEpiC	eye:	n/a
13	chr11:8969269-8969319	MCF10A-Er-Src	breast:	n/a
14	chr11:8969269-8969319	Jurkat	blood:	n/a
15	chr11:8969269-8969319	SK-N-SH	brain:	n/a
16	chr11:8969269-8969319	HRCEpiC	kidney:	n/a
17	chr11:8969269-8969319	HEEpiC	esophagus:	n/a
18	chr11:8969269-8969319	H1-hESC	embryonic stem cell:	embryo
19	chr11:8969269-8969319	MCF-7	breast:	n/a
20	chr11:8969269-8969319	SAEC	small airway:	n/a
21	chr11:8969269-8969319	CMK	blood:	n/a
22	chr11:8969269-8969319	GM12891	blood:	n/a
23	chr11:8969269-8969319	GM19239	blood:	n/a
24	chr11:8969269-8969319	HRE	kidney:	n/a
25	chr11:8969269-8969319	BJ	skin:	n/a
26	chr11:8969269-8969319	RPTEC	kidney:	n/a
27	chr11:8969269-8969319	NB4	blood:	n/a
28	chr11:8969269-8969319	AG04450	lung:	fetal
29	chr11:8969269-8969319	HRPEpiC	eye:	n/a
30	chr11:8969269-8969319	AoSMC	blood vessel:	n/a
31	chr11:8969269-8969319	GM12892	blood:	n/a
32	chr11:8969269-8969319	GM06990	blood:	n/a
33	chr11:8969269-8969319	HCF	heart:	n/a
34	chr11:8969269-8969319	AG09309	skin:	n/a
35	chr11:8969269-8969319	Hela-S3	cervix:	n/a
36	chr11:8969269-8969319	GM12878	blood:	n/a
37	chr11:8969269-8969319	AG04449	skin:	fetal
38	chr11:8969269-8969319	Hepatocyte	liver:	n/a
39	chr11:8969269-8969319	K562	blood:	n/a
40	chr11:8969269-8969319	HepG2	liver:	n/a
41	chr11:8969269-8969319	HPAEpiC	pulmonary alveolar:	n/a
42	chr11:8969269-8969319	HUVEC	blood vessel:	n/a
43	chr11:8969269-8969319	ECC-1	luminal epithelium:	n/a
44	chr11:8969269-8969319	PFSK-1	brain:	n/a
45	chr11:8969269-8969319	HCT-116	colon:	n/a
46	chr11:8969269-8969319	HCPEpiC	choroid plexus:	n/a
47	chr11:8969269-8969319	NHBE	bronchial:	n/a
48	chr11:8969269-8969319	SKMC	muscle:	n/a
49	chr11:8969269-8969319	IMR90	lung:	fetal
50	chr11:8969269-8969319	T-47D	breast:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:8968022..8970706-chr11:8976759..8978871,2	K562	blood:
2	chr11:8968144..8971876-chr11:8972662..8974412,3	K562	blood:
3	chr11:8966497..8969400-chr11:8970915..8973574,2	K562	blood:
4	chr11:8962614..8964669-chr11:8968607..8970219,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223080	TF binding region
ASCL3	TF binding region
ENSG00000223080	CpG island
ASCL3	CpG island
ENSG00000176009	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10769974	0.86[YRI][hapmap]
rs10840139	0.81[EUR][1000 genomes]
rs10840151	0.91[YRI][hapmap]
rs10840154	0.92[YRI][hapmap]
rs11042105	0.81[EUR][1000 genomes]
rs11042106	0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs11042108	0.90[JPT][hapmap]
rs11042114	0.83[EUR][1000 genomes]
rs11042115	0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs11042116	0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs11042118	0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs11042127	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042133	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042148	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1109304	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049908	0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs12223690	0.91[JPT][hapmap]
rs2163626	0.90[EUR][1000 genomes]
rs2316521	0.85[ASN][1000 genomes]
rs2455601	0.91[JPT][hapmap]
rs2568068	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568070	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568085	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568089	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568091	0.84[EUR][1000 genomes]
rs3751063	0.91[YRI][hapmap]
rs3751064	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3751066	0.83[YRI][hapmap]
rs3763911	0.92[YRI][hapmap]
rs3763912	0.91[YRI][hapmap]
rs3763913	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3763914	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815991	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4909951	0.87[YRI][hapmap]
rs56680262	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59454329	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7104661	0.91[JPT][hapmap]
rs72632952	0.82[EUR][1000 genomes]
rs7938995	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9300096	0.91[YRI][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10279	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs10279	TMEM9B-AS1	cis	lung	GTEx
rs10279	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs10279	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs10279	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs10279	TMEM9B-AS1	cis	Stomach	GTEx
rs10279	TMEM9B-AS1	cis	Thyroid	GTEx
rs10279	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs10279	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:119 , 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	chr11:8945800-8974000	Weak transcription	Colon Smooth Muscle	Colon
3	chr11:8947000-8977000	Weak transcription	Aorta	Aorta
4	chr11:8951200-8974400	Weak transcription	HepG2	liver
5	chr11:8952600-8975800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:8954400-8984400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:8955200-8976200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:8957000-8969800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:8957000-8969800	Weak transcription	Fetal Stomach	stomach
10	chr11:8957000-8974200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:8957000-8980800	Weak transcription	Fetal Heart	heart
12	chr11:8957200-8970200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr11:8957200-8973400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:8957400-8969800	Weak transcription	Spleen	Spleen
15	chr11:8959000-8974000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:8959200-8970600	Weak transcription	Fetal Kidney	kidney
17	chr11:8962800-8971800	Weak transcription	NHDF-Ad	bronchial
18	chr11:8963200-8985000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:8964000-8969800	Weak transcription	NHEK	skin
20	chr11:8965800-8984800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:8966000-8974000	Weak transcription	Brain Substantia Nigra	brain
22	chr11:8966200-8969400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:8966200-8969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:8966400-8984000	Weak transcription	Fetal Brain Male	brain
25	chr11:8966800-8969600	Weak transcription	GM12878-XiMat	blood
26	chr11:8966800-8977000	Weak transcription	Esophagus	oesophagus
27	chr11:8966800-8980800	Weak transcription	Small Intestine	intestine
28	chr11:8967200-8969600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:8967200-8969600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:8967400-8969800	Weak transcription	Fetal Intestine Small	intestine
31	chr11:8967400-8971800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr11:8967400-8975800	Weak transcription	Brain Germinal Matrix	brain
33	chr11:8967600-8970000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:8967600-8970000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr11:8967800-8969800	Weak transcription	Colonic Mucosa	Colon
36	chr11:8967800-8969800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:8968000-8970400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:8968000-8973000	Strong transcription	HSMM	muscle
39	chr11:8968000-8978200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:8968000-8978400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:8968200-8980800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:8968200-8985000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:8968400-8978600	Strong transcription	Liver	Liver
44	chr11:8968400-8979000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr11:8968400-8979200	Strong transcription	Primary B cells from cord blood	blood
46	chr11:8968600-8971200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:8968600-8976200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:8968600-8977800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr11:8968600-8978000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr11:8968600-8978000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links