Variant report

Variant	rs11601767
Chromosome Location	chr11:65316382-65316383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr11:65315836-65316393	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65265253..65270298-chr11:65311800..65316872,7	MCF-7	breast:

Variant related genes	Relation type
LTBP3	TF binding region
ENSG00000270117	Chromatin interaction
ENSG00000251562	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10896015	0.80[JPT][hapmap];0.81[TSI][hapmap]
rs10896016	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1111934	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227221	0.92[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1151517	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11604423	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11607147	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1194076	0.80[JPT][hapmap];0.81[TSI][hapmap]
rs12270054	0.80[JPT][hapmap];0.81[TSI][hapmap]
rs1787663	0.80[JPT][hapmap];0.81[TSI][hapmap]
rs3782091	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4244811	0.92[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs600231	0.86[ASW][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
4	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
5	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
6	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
7	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
8	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
9	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
10	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
11	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
12	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
13	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
14	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
15	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
16	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
17	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
18	nsv897726	chr11:65300252-65318871	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
19	nsv897728	chr11:65302893-65318871	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
20	nsv897729	chr11:65302893-65322548	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
21	nsv897730	chr11:65302893-65376484	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
22	nsv897731	chr11:65304592-65318871	Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11601767	SLC22A10	cis	parietal	SCAN
rs11601767	LTBP3	cis	cerebellum	SCAN
rs11601767	TTC9C	cis	parietal	SCAN
rs11601767	TncRNA	Cis_1M	lymphoblastoid	RTeQTL
rs11601767	NEAT1	cis	Nerve Tibial	GTEx
rs11601767	TPCN2	cis	parietal	SCAN
rs11601767	CDK2AP2	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65307200-65322600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:65308400-65319000	Weak transcription	Small Intestine	intestine
3	chr11:65309000-65318400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:65309200-65318400	Weak transcription	HUVEC	blood vessel
5	chr11:65309200-65320600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:65309200-65320600	Strong transcription	Osteobl	bone
7	chr11:65309200-65322200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:65309200-65323000	Weak transcription	Psoas Muscle	Psoas
9	chr11:65309400-65317000	Strong transcription	NHLF	lung
10	chr11:65309400-65319000	Weak transcription	NHDF-Ad	bronchial
11	chr11:65309400-65319400	Weak transcription	HSMM	muscle
12	chr11:65309400-65323000	Weak transcription	Right Atrium	heart
13	chr11:65309800-65322200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:65310200-65320400	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr11:65310200-65320800	Strong transcription	Brain Cingulate Gyrus	brain
16	chr11:65310400-65322000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:65310800-65324000	Weak transcription	Fetal Kidney	kidney
18	chr11:65311000-65317200	Weak transcription	Ovary	ovary
19	chr11:65312800-65316600	Strong transcription	A549	lung
20	chr11:65313000-65316400	Enhancers	Primary hematopoietic stem cells	blood
21	chr11:65313000-65320800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:65313200-65317000	Enhancers	Primary B cells from cord blood	blood
23	chr11:65313400-65316600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr11:65313600-65318600	Weak transcription	Brain Substantia Nigra	brain
25	chr11:65314000-65318000	Weak transcription	Aorta	Aorta
26	chr11:65314200-65318600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:65314400-65317400	Weak transcription	HepG2	liver
28	chr11:65314400-65318800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:65314600-65316800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr11:65314600-65316800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr11:65314600-65316800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr11:65314600-65316800	Enhancers	GM12878-XiMat	blood
33	chr11:65314600-65317000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr11:65314600-65317400	Strong transcription	Right Ventricle	heart
35	chr11:65314600-65317800	Weak transcription	K562	blood
36	chr11:65314600-65318000	Strong transcription	Placenta	Placenta
37	chr11:65314600-65318200	Weak transcription	Liver	Liver
38	chr11:65314600-65318200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:65314600-65318400	Weak transcription	Colonic Mucosa	Colon
40	chr11:65314600-65318400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr11:65314600-65318400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:65314600-65318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:65314600-65318600	Strong transcription	Fetal Muscle Leg	muscle
44	chr11:65314600-65318800	Weak transcription	Stomach Mucosa	stomach
45	chr11:65314600-65319000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr11:65314600-65321000	Strong transcription	Fetal Stomach	stomach
47	chr11:65314800-65316800	Strong transcription	Fetal Intestine Large	intestine
48	chr11:65314800-65317000	Strong transcription	Lung	lung
49	chr11:65314800-65317400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:65314800-65317600	Enhancers	Primary B cells from peripheral blood	blood

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