Variant report

Variant	rs667126
Chromosome Location	chr11:68177728-68177729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1784235	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306862	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2472415	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2508834	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs314750	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs3736228	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs3781586	0.93[JPT][hapmap]
rs41478448	0.88[ASN][1000 genomes]
rs475712	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491347	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs531163	0.93[CHB][hapmap]
rs546803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs554734	0.93[CHB][hapmap]
rs556442	0.93[CHB][hapmap]
rs56400711	0.88[ASN][1000 genomes]
rs576118	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599083	0.93[CHB][hapmap]
rs607887	0.93[CHB][hapmap]
rs608343	0.93[CHB][hapmap];0.82[CHD][hapmap]
rs630225	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs638076	0.93[CHB][hapmap]
rs640569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591339	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685095	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs686921	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs689179	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102451	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs880610	0.80[ASN][1000 genomes]
rs901823	0.85[CHB][hapmap]
rs923346	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
14	nsv555285	chr11:68144283-68231240	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv468618	chr11:68171013-68231240	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers 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	10 gene(s)	inside rSNPs	diseases
16	esv3336346	chr11:68175876-68177824	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs667126	LRP5	cis	lymphoblastoid	seeQTL
rs667126	RBM4B	cis	cerebellum	SCAN
rs667126	GAL	cis	parietal	SCAN
rs667126	CPT1A	cis	multi-tissue	Pritchard
rs667126	MTL5	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68142600-68179000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:68147400-68181600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:68148600-68196800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:68149600-68180400	Weak transcription	NHLF	lung
5	chr11:68157200-68196600	Weak transcription	NH-A	brain
6	chr11:68157600-68180400	Weak transcription	Osteobl	bone
7	chr11:68165800-68178400	Weak transcription	Brain Angular Gyrus	brain
8	chr11:68167200-68179600	Weak transcription	K562	blood
9	chr11:68167800-68178600	Weak transcription	Psoas Muscle	Psoas
10	chr11:68167800-68181000	Weak transcription	Small Intestine	intestine
11	chr11:68167800-68196600	Weak transcription	Fetal Brain Male	brain
12	chr11:68168400-68185000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:68168400-68189000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:68168600-68181400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:68168600-68188800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:68168600-68188800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:68168600-68193600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:68168600-68195600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:68169000-68193600	Strong transcription	Fetal Intestine Small	intestine
20	chr11:68169200-68180200	Strong transcription	Fetal Stomach	stomach
21	chr11:68169200-68180800	Strong transcription	Adipose Nuclei	Adipose
22	chr11:68169400-68181400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:68169400-68181600	Strong transcription	Thymus	Thymus
24	chr11:68169400-68196600	Weak transcription	Right Atrium	heart
25	chr11:68169600-68188200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:68169600-68196800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:68171400-68178000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:68171800-68179600	Weak transcription	Fetal Kidney	kidney
29	chr11:68172200-68178600	Weak transcription	HSMM	muscle
30	chr11:68172200-68180200	Weak transcription	NHDF-Ad	bronchial
31	chr11:68173000-68184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:68173000-68188400	Strong transcription	Dnd41	blood
33	chr11:68173400-68184200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:68173400-68187400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:68173600-68180200	Weak transcription	Fetal Heart	heart
36	chr11:68173800-68177800	Weak transcription	Brain Hippocampus Middle	brain
37	chr11:68173800-68189000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:68174000-68178800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:68174000-68180200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr11:68174000-68181400	Strong transcription	Fetal Thymus	thymus
41	chr11:68174400-68178200	Weak transcription	Stomach Mucosa	stomach
42	chr11:68174400-68178600	Strong transcription	Liver	Liver
43	chr11:68174400-68179400	Weak transcription	GM12878-XiMat	blood
44	chr11:68174400-68180200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr11:68174400-68192800	Strong transcription	Fetal Intestine Large	intestine
46	chr11:68174400-68195800	Weak transcription	Primary B cells from cord blood	blood
47	chr11:68174600-68180400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:68174600-68196800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:68175200-68178000	Strong transcription	HMEC	breast
50	chr11:68175200-68180400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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