Variant report

Variant	rs9874211
Chromosome Location	chr3:137835032-137835033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:137833245-137835104	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:137832958-137835110	IMR90	lung:	n/a	n/a
3	CEBPB	chr3:137833758-137835222	Hela-S3	cervix:	n/a	chr3:137835056-137835069
4	POLR2A	chr3:137833776-137835188	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
DZIP1L	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1107422	0.81[ASN][1000 genomes]
rs13100360	0.84[ASN][1000 genomes]
rs1351446	0.90[ASN][1000 genomes]
rs1545816	0.84[ASN][1000 genomes]
rs1564496	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17838821	0.84[ASN][1000 genomes]
rs2170309	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2246945	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622694	0.83[AMR][1000 genomes]
rs2622695	0.80[AMR][1000 genomes]
rs2622697	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622698	0.90[ASN][1000 genomes]
rs2622699	0.82[AMR][1000 genomes]
rs2622711	0.81[ASN][1000 genomes]
rs2622714	0.83[ASN][1000 genomes]
rs2622715	0.83[ASN][1000 genomes]
rs2622716	0.83[ASN][1000 genomes]
rs2622717	0.83[ASN][1000 genomes]
rs2622718	0.83[ASN][1000 genomes]
rs2622719	0.84[ASN][1000 genomes]
rs2622720	0.84[ASN][1000 genomes]
rs2622727	0.84[ASN][1000 genomes]
rs2622728	0.84[ASN][1000 genomes]
rs2622729	0.84[ASN][1000 genomes]
rs2622730	0.87[ASN][1000 genomes]
rs2622745	0.86[ASN][1000 genomes]
rs2622746	0.91[ASN][1000 genomes]
rs2724679	0.82[ASN][1000 genomes]
rs2724687	0.90[ASN][1000 genomes]
rs2724690	0.83[AMR][1000 genomes]
rs2724693	0.83[ASN][1000 genomes]
rs2724694	0.84[ASN][1000 genomes]
rs2724716	0.84[ASN][1000 genomes]
rs2724717	0.87[ASN][1000 genomes]
rs2724729	0.91[ASN][1000 genomes]
rs28480035	0.80[ASN][1000 genomes]
rs329381	0.84[ASN][1000 genomes]
rs329382	0.82[ASN][1000 genomes]
rs329383	0.83[ASN][1000 genomes]
rs329384	0.84[ASN][1000 genomes]
rs329385	0.84[ASN][1000 genomes]
rs367439	0.84[ASN][1000 genomes]
rs390729	0.87[ASN][1000 genomes]
rs405265	0.87[ASN][1000 genomes]
rs4678403	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6809258	0.81[ASN][1000 genomes]
rs7613558	0.83[AMR][1000 genomes]
rs7613955	0.87[ASN][1000 genomes]
rs7629243	0.84[ASN][1000 genomes]
rs7639197	0.83[ASN][1000 genomes]
rs899983	0.81[ASN][1000 genomes]
rs9812778	0.90[ASN][1000 genomes]
rs9834462	0.91[ASN][1000 genomes]
rs9842648	0.92[ASN][1000 genomes]
rs9842918	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9857908	0.92[ASN][1000 genomes]
rs9860229	0.91[ASN][1000 genomes]
rs9860630	0.88[ASN][1000 genomes]
rs996432	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007857	chr3:137767454-137843106	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9874211	A4GNT	cis	Nerve Tibial	GTEx
rs9874211	A4GNT	cis	Thyroid	GTEx
rs9874211	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137833000-137835200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:137833200-137835200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:137833400-137835200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:137833400-137835200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
5	chr3:137833400-137835200	Active TSS	Fetal Kidney	kidney
6	chr3:137833400-137835400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:137833400-137835400	Active TSS	A549	lung
8	chr3:137833600-137835200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:137833600-137835200	Active TSS	Fetal Lung	lung
10	chr3:137833800-137835200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:137833800-137835200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:137833800-137835200	Active TSS	Colon Smooth Muscle	Colon
13	chr3:137833800-137835200	Active TSS	HSMMtube	muscle
14	chr3:137834000-137835200	Active TSS	Fetal Brain Female	brain
15	chr3:137834600-137835200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:137834600-137835200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:137834600-137835200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:137834800-137835200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:137834800-137835200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:137834800-137835200	Enhancers	Fetal Muscle Trunk	muscle
21	chr3:137834800-137835200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:137834800-137835200	Flanking Active TSS	Hela-S3	cervix
23	chr3:137834800-137835200	Flanking Active TSS	NH-A	brain
24	chr3:137834800-137835400	Enhancers	HUVEC	blood vessel
25	chr3:137834800-137835800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:137834800-137835800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:137834800-137837400	Weak transcription	Pancreas	Pancrea
28	chr3:137834800-137837600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:137834800-137837600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:137834800-137837600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:137834800-137837600	Weak transcription	HSMM	muscle
32	chr3:137834800-137837800	Weak transcription	Spleen	Spleen
33	chr3:137834800-137843000	Weak transcription	Placenta	Placenta
34	chr3:137834800-137843600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:137835000-137835200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr3:137835000-137835200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:137835000-137835200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr3:137835000-137835200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr3:137835000-137835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:137835000-137835200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:137835000-137835200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr3:137835000-137835200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr3:137835000-137835200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:137835000-137835200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr3:137835000-137835200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:137835000-137835200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:137835000-137835200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:137835000-137835200	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr3:137835000-137835200	Enhancers	Brain Angular Gyrus	brain
50	chr3:137835000-137835200	Enhancers	Fetal Heart	heart

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