Variant report

Variant	rs4678403
Chromosome Location	chr3:137837557-137837558
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	RAD21	chr3:137837473-137838190	HCT-116	colon:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
2	RAD21	chr3:137837549-137838078	SK-N-SH_RA	brain:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
3	RAD21	chr3:137837452-137838522	SK-N-SH	brain:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
4	CTCF	chr3:137837500-137837650	WERI-Rb-1	eye:	n/a	n/a
5	RCOR1	chr3:137837462-137837968	HepG2	liver:	n/a	n/a
6	CTCF	chr3:137837437-137838465	SK-N-SH	brain:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
7	SMC3	chr3:137837114-137838521	SK-N-SH	brain:	n/a	chr3:137838445-137838455 chr3:137837906-137837920
8	RAD21	chr3:137837539-137838229	A549	lung:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
9	BRCA1	chr3:137837524-137837565	GM12878	blood:	n/a	n/a
10	RAD21	chr3:137837539-137838176	ECC-1	luminal epithelium:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
11	RAD21	chr3:137837475-137838307	HCT-116	colon:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
12	CTCF	chr3:137837525-137838362	A549	lung:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
13	RAD21	chr3:137837545-137838190	MCF-7	breast:	n/a	chr3:137837902-137837921 chr3:137837904-137837916

No.	Distal block	Cell Line	Cell type
1	chr3:137820273..137821044-chr3:137837392..137837964,2	MCF-7	breast:
2	chr3:137786807..137788879-chr3:137836537..137838505,22	MCF-7	breast:
3	chr3:137785795..137788680-chr3:137836157..137838933,3	MCF-7	breast:
4	chr3:137787211..137788408-chr3:137837411..137838466,26	MCF-7	breast:
5	chr3:137789176..137789822-chr3:137837460..137838165,2	MCF-7	breast:
6	chr3:137787348..137788077-chr3:137837494..137838376,4	K562	blood:

Variant related genes	Relation type
DZIP1L	TF binding region
ENSG00000158163	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1107422	0.85[ASN][1000 genomes]
rs11719358	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs13100360	0.88[ASN][1000 genomes]
rs1351446	0.97[ASN][1000 genomes]
rs1545816	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1564496	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17838821	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs179282	0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2170309	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219936	0.88[MEX][hapmap]
rs2246945	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622694	0.88[MEX][hapmap];0.80[AMR][1000 genomes]
rs2622695	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs2622697	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622698	0.97[ASN][1000 genomes]
rs2622704	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2622705	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2622706	0.80[ASN][1000 genomes]
rs2622707	0.80[ASN][1000 genomes]
rs2622709	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2622710	0.83[ASN][1000 genomes]
rs2622711	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2622714	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622715	0.86[ASN][1000 genomes]
rs2622716	0.86[ASN][1000 genomes]
rs2622717	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622718	0.86[ASN][1000 genomes]
rs2622719	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622720	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622727	0.88[ASN][1000 genomes]
rs2622728	0.88[ASN][1000 genomes]
rs2622729	0.88[ASN][1000 genomes]
rs2622730	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2622745	0.89[ASN][1000 genomes]
rs2622746	0.95[ASN][1000 genomes]
rs2724679	0.87[ASN][1000 genomes]
rs2724687	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2724690	0.80[AMR][1000 genomes]
rs2724692	0.88[MEX][hapmap]
rs2724693	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2724694	0.88[ASN][1000 genomes]
rs2724697	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2724698	0.80[ASN][1000 genomes]
rs2724699	0.80[ASN][1000 genomes]
rs2724700	0.80[ASN][1000 genomes]
rs2724701	0.80[ASN][1000 genomes]
rs2724702	0.80[ASN][1000 genomes]
rs2724703	0.83[ASN][1000 genomes]
rs2724704	0.80[ASN][1000 genomes]
rs2724705	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2724706	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2724707	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2724708	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2724716	0.88[ASN][1000 genomes]
rs2724717	0.90[ASN][1000 genomes]
rs2724729	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28480035	0.84[ASN][1000 genomes]
rs329381	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs329382	0.85[ASN][1000 genomes]
rs329383	0.86[ASN][1000 genomes]
rs329384	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs329385	0.88[ASN][1000 genomes]
rs329388	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs329389	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs329390	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs329391	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs365504	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs367439	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs374045	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs382629	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs384828	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs389697	0.80[ASN][1000 genomes]
rs390729	0.90[ASN][1000 genomes]
rs405265	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs405602	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs407009	0.80[ASN][1000 genomes]
rs419075	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs425938	0.83[ASN][1000 genomes]
rs442800	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs445025	0.83[ASN][1000 genomes]
rs446644	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs452195	0.80[ASN][1000 genomes]
rs453023	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs618553	0.83[ASN][1000 genomes]
rs6809258	0.86[ASN][1000 genomes]
rs7613558	0.80[AMR][1000 genomes]
rs7613955	0.90[ASN][1000 genomes]
rs7629243	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7639197	0.86[ASN][1000 genomes]
rs774814	0.84[MEX][hapmap]
rs811811	0.83[MEX][hapmap]
rs899983	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9812778	0.93[ASN][1000 genomes]
rs9834462	0.95[ASN][1000 genomes]
rs9842648	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9842918	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9857908	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9860229	0.95[ASN][1000 genomes]
rs9860630	0.91[ASN][1000 genomes]
rs9874211	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs996432	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[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
rs4678403	A4GNT	cis	Nerve Tibial	GTEx
rs4678403	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs4678403	A4GNT	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137834800-137837600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:137834800-137837600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:137834800-137837600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:137834800-137837600	Weak transcription	HSMM	muscle
5	chr3:137834800-137837800	Weak transcription	Spleen	Spleen
6	chr3:137834800-137843000	Weak transcription	Placenta	Placenta
7	chr3:137834800-137843600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:137835000-137837600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:137835000-137837600	Weak transcription	Stomach Mucosa	stomach
10	chr3:137835000-137837600	Weak transcription	HMEC	breast
11	chr3:137835000-137843600	Weak transcription	Right Ventricle	heart
12	chr3:137835200-137837600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:137835200-137837600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:137835200-137837600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:137835200-137837600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:137835200-137837600	Weak transcription	Fetal Stomach	stomach
17	chr3:137835200-137843200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:137835200-137843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:137835200-137843600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:137835200-137843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:137835400-137837600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:137835400-137837600	Weak transcription	Hela-S3	cervix
23	chr3:137835400-137843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:137835400-137844200	Weak transcription	A549	lung
25	chr3:137835800-137843600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:137836800-137838000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:137836800-137838000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:137836800-137838000	Enhancers	Adipose Nuclei	Adipose
29	chr3:137837000-137838000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:137837200-137837600	Enhancers	HepG2	liver
31	chr3:137837200-137838200	Enhancers	Fetal Heart	heart
32	chr3:137837400-137837600	Flanking Active TSS	Fetal Kidney	kidney
33	chr3:137837400-137837800	Enhancers	Pancreas	Pancrea
34	chr3:137837400-137838000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:137837400-137838000	Enhancers	NHDF-Ad	bronchial
36	chr3:137837400-137838000	Enhancers	NHLF	lung
37	chr3:137837400-137838000	Enhancers	Osteobl	bone
38	chr3:137837400-137838400	Enhancers	Fetal Muscle Leg	muscle
39	chr3:137837400-137838600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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