Variant report

Variant	rs13438432
Chromosome Location	chr7:66280002-66280003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10224536	0.82[EUR][1000 genomes]
rs10225392	0.81[EUR][1000 genomes]
rs10229580	0.81[EUR][1000 genomes]
rs10231411	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10231860	0.83[EUR][1000 genomes]
rs10234322	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10234747	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235037	0.83[EUR][1000 genomes]
rs10235638	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10240153	0.81[EUR][1000 genomes]
rs10240582	0.81[EUR][1000 genomes]
rs10241395	0.84[EUR][1000 genomes]
rs10241528	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10242870	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10243608	0.84[EUR][1000 genomes]
rs10244459	0.84[EUR][1000 genomes]
rs10247324	0.88[EUR][1000 genomes]
rs10250124	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10252133	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10256117	0.82[EUR][1000 genomes]
rs10257393	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10258628	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10262184	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10263993	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10265069	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10267253	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10267834	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10270326	0.82[EUR][1000 genomes]
rs10271177	0.81[EUR][1000 genomes]
rs10273320	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10278343	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10281090	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10282310	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282522	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10479728	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1060527	0.88[EUR][1000 genomes]
rs1064795	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12234826	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12333749	0.81[EUR][1000 genomes]
rs12334214	0.83[EUR][1000 genomes]
rs17138274	0.81[EUR][1000 genomes]
rs2013707	0.85[EUR][1000 genomes]
rs28368585	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28375318	0.83[EUR][1000 genomes]
rs28379824	0.89[EUR][1000 genomes]
rs28460006	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28533332	0.88[EUR][1000 genomes]
rs28547918	0.87[EUR][1000 genomes]
rs28560293	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28607736	0.82[EUR][1000 genomes]
rs28634091	0.89[EUR][1000 genomes]
rs28663128	0.87[EUR][1000 genomes]
rs3778907	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778908	0.88[EUR][1000 genomes]
rs3800814	0.89[EUR][1000 genomes]
rs3823607	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823609	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3962133	0.84[EUR][1000 genomes]
rs4718417	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60972148	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67408913	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6973897	0.81[EUR][1000 genomes]
rs6974601	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73133851	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73135960	0.81[EUR][1000 genomes]
rs73137960	0.82[EUR][1000 genomes]
rs73137963	0.81[EUR][1000 genomes]
rs73139941	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73139976	0.84[EUR][1000 genomes]
rs73143998	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7455757	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7777631	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7796977	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv981513	chr7:66276464-66291614	Weak transcription Enhancers Strong transcription Genic enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13438432	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs13438432	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66261000-66281400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:66275600-66280600	Weak transcription	Brain Anterior Caudate	brain
3	chr7:66275600-66281200	Weak transcription	Right Ventricle	heart
4	chr7:66275800-66280600	Weak transcription	Spleen	Spleen
5	chr7:66276000-66280400	Weak transcription	Pancreas	Pancrea
6	chr7:66276000-66282200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:66276000-66282800	Weak transcription	Brain Germinal Matrix	brain
8	chr7:66276200-66282000	Weak transcription	GM12878-XiMat	blood
9	chr7:66276200-66282200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:66276400-66280600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr7:66276400-66281000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:66276600-66281200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr7:66276800-66280200	Weak transcription	Fetal Intestine Large	intestine
14	chr7:66276800-66281200	Weak transcription	Fetal Thymus	thymus
15	chr7:66276800-66284800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:66277000-66281200	Weak transcription	HMEC	breast
17	chr7:66277000-66282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:66277000-66282000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr7:66277000-66282200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:66277200-66280600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:66277200-66281200	Weak transcription	NHEK	skin
22	chr7:66277200-66282200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:66277200-66282200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:66277400-66281400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:66277600-66280600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr7:66277600-66281000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:66277800-66280800	Weak transcription	Osteobl	bone
28	chr7:66277800-66284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:66277800-66288600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr7:66278400-66280200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:66278400-66281000	Weak transcription	Fetal Muscle Leg	muscle
32	chr7:66278400-66282000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr7:66278400-66282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:66278400-66282200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:66278400-66282200	Weak transcription	HepG2	liver
36	chr7:66278600-66280200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:66278600-66280200	Weak transcription	HSMM	muscle
38	chr7:66278600-66280200	Weak transcription	NHLF	lung
39	chr7:66278600-66280400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:66278600-66280400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:66278600-66281200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:66278600-66281400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:66278600-66282200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr7:66278600-66282200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr7:66278600-66282200	Weak transcription	Adipose Nuclei	Adipose
46	chr7:66278600-66282200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr7:66278600-66282200	Weak transcription	HSMMtube	muscle
48	chr7:66278800-66282000	Weak transcription	Fetal Intestine Small	intestine
49	chr7:66278800-66284800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:66279000-66283400	Weak transcription	Fetal Stomach	stomach

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