Variant report

Variant	rs17149027
Chromosome Location	chr11:68142656-68142657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:68142620..68145092-chr11:68154931..68156439,2	K562	blood:
2	chr11:68142032..68143700-chr11:68144005..68145660,2	K562	blood:
3	chr11:68139963..68143700-chr11:68143791..68147570,5	K562	blood:
4	chr11:68125238..68127022-chr11:68141458..68143757,2	K562	blood:
5	chr11:68109553..68111761-chr11:68141743..68145127,3	MCF-7	breast:
6	chr11:68133350..68135740-chr11:68141722..68144465,3	MCF-7	breast:
7	chr11:68099361..68102252-chr11:68142403..68144649,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11574424	0.86[AFR][1000 genomes]
rs17149031	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149041	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149042	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17159533	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2089915	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58373012	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58500312	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58779840	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59682172	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60632461	1.00[EUR][1000 genomes]
rs61101778	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61132569	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61539720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7101866	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7102311	0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7111735	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7112824	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7122741	1.00[AMR][1000 genomes]
rs73515038	1.00[EUR][1000 genomes]
rs73515041	1.00[EUR][1000 genomes]
rs7939653	1.00[EUR][1000 genomes]
rs7939672	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7940269	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7947068	0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	esv3347272	chr11:67969427-68218997	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv897857	chr11:68056770-68231240	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv897858	chr11:68077238-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv897859	chr11:68102000-68231240	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv897860	chr11:68102000-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1047532	chr11:68103330-68239242	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv541082	chr11:68103330-68239242	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1039671	chr11:68120571-68206630	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1036561	chr11:68123135-68315685	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv897861	chr11:68129606-68196830	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak 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	5 gene(s)	inside rSNPs	diseases
12	nsv897862	chr11:68129606-68236389	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv469965	chr11:68140781-68217420	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17149027	LRP5	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68121600-68148200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:68121800-68156400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr11:68124800-68146600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:68128200-68153800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr11:68129800-68153600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:68131800-68143400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:68135200-68147600	Weak transcription	Primary T cells from cord blood	blood
8	chr11:68135200-68153400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:68135200-68153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:68136200-68153400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:68136600-68143600	Enhancers	Placenta	Placenta
12	chr11:68136600-68145600	Enhancers	Left Ventricle	heart
13	chr11:68136800-68143400	Enhancers	Fetal Heart	heart
14	chr11:68136800-68152800	Weak transcription	Dnd41	blood
15	chr11:68137000-68156400	Weak transcription	K562	blood
16	chr11:68137400-68143600	Genic enhancers	Duodenum Mucosa	Duodenum
17	chr11:68138800-68143600	Enhancers	Right Atrium	heart
18	chr11:68139000-68142800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:68139200-68142800	Enhancers	Primary B cells from cord blood	blood
20	chr11:68139200-68144400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr11:68139200-68145800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:68139600-68156400	Weak transcription	Hela-S3	cervix
23	chr11:68139800-68143200	Enhancers	Ovary	ovary
24	chr11:68140000-68142800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:68140000-68143000	Enhancers	Fetal Lung	lung
26	chr11:68140000-68143400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr11:68140000-68144600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:68140000-68147600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:68140000-68147800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:68140000-68150200	Enhancers	Lung	lung
31	chr11:68140000-68153400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr11:68140200-68153600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:68140400-68142800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:68140400-68143400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:68140600-68143000	Enhancers	Brain Cingulate Gyrus	brain
36	chr11:68140600-68143200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:68140800-68142800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
38	chr11:68140800-68142800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:68140800-68142800	Enhancers	Esophagus	oesophagus
40	chr11:68140800-68143200	Enhancers	Fetal Brain Male	brain
41	chr11:68140800-68143200	Enhancers	Small Intestine	intestine
42	chr11:68140800-68143600	Enhancers	Stomach Mucosa	stomach
43	chr11:68141000-68142800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:68141000-68142800	Enhancers	Brain Angular Gyrus	brain
45	chr11:68141000-68143200	Enhancers	Psoas Muscle	Psoas
46	chr11:68141200-68148200	Weak transcription	Aorta	Aorta
47	chr11:68141400-68143200	Genic enhancers	Colonic Mucosa	Colon
48	chr11:68141400-68153400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:68141600-68143400	Enhancers	Brain Anterior Caudate	brain
50	chr11:68141800-68142800	Enhancers	Brain Hippocampus Middle	brain

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