Variant report

Variant	rs12752829
Chromosome Location	chr1:175880101-175880102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10913093	0.85[EUR][1000 genomes]
rs10913100	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805196	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807032	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239742	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12406237	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12409939	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724711	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726210	0.93[EUR][1000 genomes]
rs12726737	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12728682	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730153	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12730725	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12735431	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12736942	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12738956	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740514	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745657	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752542	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12753832	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754330	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12755734	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12757152	0.85[EUR][1000 genomes]
rs12758770	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12759426	0.83[EUR][1000 genomes]
rs12759478	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12759736	0.86[EUR][1000 genomes]
rs1303987	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57385190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687954	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71514835	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525623	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528198	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7534440	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555561	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33328	chr1:175446583-175910001	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv3344055	chr1:175873040-175887908	Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175863200-175906400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:175874400-175945600	Weak transcription	A549	lung
3	chr1:175875000-175882800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:175877400-175894600	Weak transcription	HSMM	muscle
5	chr1:175877800-175902400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:175879400-175880200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:175879400-175880200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:175879400-175880200	ZNF genes & repeats	Left Ventricle	heart
9	chr1:175879400-175880200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
10	chr1:175879400-175880200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
11	chr1:175879400-175880400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:175879400-175880400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:175879400-175880400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:175879400-175880400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:175879400-175880400	ZNF genes & repeats	Aorta	Aorta
16	chr1:175879400-175880400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:175879400-175880400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
18	chr1:175879400-175880400	ZNF genes & repeats	Lung	lung
19	chr1:175879400-175880400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
20	chr1:175879400-175880600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
21	chr1:175879400-175880600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr1:175879400-175880600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
23	chr1:175879400-175880600	ZNF genes & repeats	Fetal Muscle Leg	muscle
24	chr1:175879400-175881000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:175879400-175881000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:175879400-175881200	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr1:175879400-175881400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:175879400-175882000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:175879400-175882600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:175879600-175880200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:175879600-175880400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:175879600-175881000	ZNF genes & repeats	Brain Angular Gyrus	brain
33	chr1:175879800-175896000	Weak transcription	Fetal Stomach	stomach
34	chr1:175880000-175880600	ZNF genes & repeats	GM12878-XiMat	blood
35	chr1:175880000-175897200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:175880000-175897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:175880000-175937800	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links