Variant report

Variant	rs17146964
Chromosome Location	chr11:65249145-65249146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
2	chr11:65249004..65251307-chr20:62128921..62131592,2	MCF-7	breast:
3	chr11:65247365..65249731-chrX:107327338..107328859,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LTBP3-6	chr11:65248971-65249339	NONHSAT022122

Variant related genes	Relation type
ENSG00000101210	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1075692	0.86[ASN][1000 genomes]
rs10896004	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896005	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896006	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896007	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896009	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896010	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896012	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.83[ASN][1000 genomes]
rs10896015	0.82[MEX][hapmap]
rs11227196	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227197	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227198	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227200	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11227201	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227202	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227205	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11227206	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1152619	0.86[CEU][hapmap]
rs1194076	0.82[MEX][hapmap]
rs12269965	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12269975	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12270054	0.87[MEX][hapmap]
rs12294910	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12360896	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12364730	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12788055	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12803915	0.86[ASN][1000 genomes]
rs12808303	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1346	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1783541	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs2508710	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3200401	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs34512931	0.82[ASN][1000 genomes]
rs34527830	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34582634	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34877911	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35292734	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35469818	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35826299	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825071	0.84[ASN][1000 genomes]
rs4102217	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57311037	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7128776	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931615	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7935551	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs947791	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic 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	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong 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	474 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	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
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	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
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
17	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
18	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
19	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
20	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
21	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

Variant related diseases (count:1)

Disease	PMID	Source
Vertical cup-disc ratio	20548946	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17146964	ATG2A	cis	lymphoblastoid	seeQTL
rs17146964	SNX32	cis	parietal	SCAN
rs17146964	BBS1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65245400-65254600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:65245600-65252200	Weak transcription	Small Intestine	intestine
3	chr11:65245600-65255600	Weak transcription	Gastric	stomach
4	chr11:65246400-65250200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:65246400-65254200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:65246400-65254800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr11:65246800-65250400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr11:65247200-65251200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:65247400-65249200	Weak transcription	Aorta	Aorta
10	chr11:65247400-65249400	Enhancers	Brain Substantia Nigra	brain
11	chr11:65247400-65250000	Enhancers	Colon Smooth Muscle	Colon
12	chr11:65247400-65250000	Enhancers	HSMM	muscle
13	chr11:65247400-65252200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:65247400-65254800	Weak transcription	Spleen	Spleen
15	chr11:65247600-65249200	Weak transcription	Left Ventricle	heart
16	chr11:65247600-65249600	Enhancers	NHDF-Ad	bronchial
17	chr11:65247600-65250200	Weak transcription	Fetal Brain Female	brain
18	chr11:65247600-65251000	Weak transcription	Fetal Brain Male	brain
19	chr11:65247600-65252400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:65247600-65252600	Weak transcription	Fetal Intestine Small	intestine
21	chr11:65247600-65252600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:65247600-65252800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:65247600-65252800	Weak transcription	Liver	Liver
24	chr11:65247600-65252800	Weak transcription	Brain Germinal Matrix	brain
25	chr11:65247600-65254000	Weak transcription	Psoas Muscle	Psoas
26	chr11:65247600-65254200	Weak transcription	Fetal Intestine Large	intestine
27	chr11:65247800-65249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:65247800-65249800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:65247800-65250200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:65247800-65250200	Enhancers	HSMMtube	muscle
31	chr11:65247800-65250200	Enhancers	Osteobl	bone
32	chr11:65247800-65250400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:65247800-65251400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:65247800-65252200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr11:65247800-65252600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:65247800-65252800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:65247800-65253000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr11:65247800-65253000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:65247800-65253400	Weak transcription	Right Ventricle	heart
40	chr11:65247800-65254200	Weak transcription	Fetal Lung	lung
41	chr11:65247800-65254400	Weak transcription	Colonic Mucosa	Colon
42	chr11:65247800-65254400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr11:65248000-65252400	Weak transcription	Stomach Mucosa	stomach
44	chr11:65248000-65252600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:65248400-65249200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:65248400-65249600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:65248600-65249400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:65248600-65250200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:65248600-65250200	Enhancers	NHEK	skin
50	chr11:65248800-65249200	Active TSS	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links