Variant report

Variant	rs7112824
Chromosome Location	chr11:68135890-68135891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:68135719..68138627-chr11:68149871..68152730,2	MCF-7	breast:
2	chr11:68134335..68136167-chr11:68137890..68139982,2	K562	blood:
3	chr11:68125237..68127996-chr11:68134543..68137773,3	K562	blood:
4	chr11:68108931..68115142-chr11:68135401..68140500,11	MCF-7	breast:
5	chr11:68093866..68096546-chr11:68134351..68136830,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11574424	0.94[AFR][1000 genomes]
rs17149027	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149031	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149041	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17149042	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17159533	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2089915	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58373012	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58500312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58779840	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59682172	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60632461	1.00[EUR][1000 genomes]
rs61101778	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61132569	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61539720	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7101866	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7102311	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7111735	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7122741	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73515038	1.00[EUR][1000 genomes]
rs73515041	1.00[EUR][1000 genomes]
rs7939653	1.00[EUR][1000 genomes]
rs7939672	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7940269	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7947068	1.00[ASW][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7112824	LRP5	cis	lymphoblastoid	seeQTL
rs7112824	LRP5	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68110600-68137800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:68111200-68137400	Weak transcription	Brain Hippocampus Middle	brain
3	chr11:68114800-68138000	Weak transcription	Fetal Kidney	kidney
4	chr11:68121600-68148200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:68121800-68137400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:68121800-68156400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:68122000-68137800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:68122200-68139800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:68122600-68138200	Weak transcription	HUVEC	blood vessel
10	chr11:68122800-68137200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:68123200-68136800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:68123200-68137000	Weak transcription	Psoas Muscle	Psoas
13	chr11:68123200-68137200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:68123200-68139600	Weak transcription	Brain Substantia Nigra	brain
15	chr11:68123400-68136000	Strong transcription	Fetal Muscle Leg	muscle
16	chr11:68124000-68137400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr11:68124800-68146600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:68125200-68136000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:68125800-68136000	Strong transcription	Right Ventricle	heart
20	chr11:68126000-68136600	Weak transcription	Right Atrium	heart
21	chr11:68126200-68136200	Strong transcription	Liver	Liver
22	chr11:68126200-68136800	Weak transcription	Fetal Heart	heart
23	chr11:68126600-68137200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:68126600-68137600	Weak transcription	NHLF	lung
25	chr11:68126800-68137400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:68126800-68138200	Weak transcription	HSMM	muscle
27	chr11:68126800-68138200	Weak transcription	NH-A	brain
28	chr11:68127000-68136600	Weak transcription	K562	blood
29	chr11:68127000-68137200	Weak transcription	Brain Anterior Caudate	brain
30	chr11:68127000-68137600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:68127000-68137800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:68127000-68138000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:68127000-68140800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:68128000-68140800	Weak transcription	Fetal Brain Male	brain
35	chr11:68128200-68136800	Weak transcription	Aorta	Aorta
36	chr11:68128200-68140800	Weak transcription	Osteobl	bone
37	chr11:68128200-68153800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:68129600-68136800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:68129600-68137200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:68129600-68137600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:68129600-68137800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:68129600-68139400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:68129800-68153600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:68130800-68137200	Strong transcription	Fetal Stomach	stomach
45	chr11:68131200-68136000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr11:68131800-68136000	Strong transcription	Brain Germinal Matrix	brain
47	chr11:68131800-68143400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:68132000-68136000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:68132000-68136200	Strong transcription	Fetal Thymus	thymus
50	chr11:68132000-68140400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links