Variant report

Variant	rs2929346
Chromosome Location	chr3:19979487-19979488
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	GATA1	chr3:19978818-19979778	PBDE	blood:	n/a	chr3:19979180-19979190 chr3:19979214-19979223 chr3:19979211-19979220 chr3:19979071-19979082 chr3:19979075-19979084 chr3:19979221-19979237
2	TEAD4	chr3:19978882-19979568	K562	blood:	n/a	n/a
3	ATF1	chr3:19978931-19979563	K562	blood:	n/a	n/a
4	STAT5A	chr3:19979035-19979587	K562	blood:	n/a	chr3:19979301-19979313
5	HDAC2	chr3:19979156-19979489	K562	blood:	n/a	chr3:19979175-19979189
6	TAL1	chr3:19978937-19979547	K562	blood:	n/a	chr3:19979074-19979082
7	NR2F2	chr3:19978957-19979527	K562	blood:	n/a	n/a
8	JUND	chr3:19978811-19979724	K562	blood:	n/a	chr3:19979212-19979222 chr3:19979212-19979222 chr3:19979213-19979221 chr3:19979211-19979223 chr3:19979212-19979222 chr3:19978813-19978822
9	MYC	chr3:19978833-19979487	K562	blood:	n/a	n/a
10	BHLHE40	chr3:19978841-19979677	K562	blood:	n/a	n/a
11	IRF1	chr3:19978945-19979604	K562	blood:	n/a	n/a
12	TBL1XR1	chr3:19979008-19979735	K562	blood:	n/a	n/a
13	GATA3	chr3:19978914-19979534	SK-N-SH	brain:	n/a	chr3:19979180-19979190 chr3:19979214-19979223 chr3:19979211-19979220 chr3:19979071-19979082 chr3:19979075-19979084 chr3:19979221-19979237
14	TEAD4	chr3:19978757-19979733	K562	blood:	n/a	chr3:19979639-19979648
15	IRF1	chr3:19978761-19979579	K562	blood:	n/a	n/a
16	RCOR1	chr3:19978867-19980107	K562	blood:	n/a	n/a
17	CEBPD	chr3:19978958-19979575	K562	blood:	n/a	n/a
18	JUN	chr3:19978978-19979500	K562	blood:	n/a	chr3:19979212-19979222 chr3:19979212-19979222 chr3:19979213-19979221 chr3:19979211-19979223 chr3:19979212-19979222
19	ZNF143	chr3:19979116-19979611	K562	blood:	n/a	n/a
20	ARID3A	chr3:19978769-19979488	K562	blood:	n/a	n/a
21	PML	chr3:19978790-19979505	K562	blood:	n/a	n/a
22	HCFC1	chr3:19979210-19979751	K562	blood:	n/a	n/a
23	CBX3	chr3:19978710-19979491	K562	blood:	n/a	n/a
24	JUN	chr3:19978875-19979492	K562	blood:	n/a	chr3:19979212-19979222 chr3:19979212-19979222 chr3:19979213-19979221 chr3:19979211-19979223 chr3:19979212-19979222
25	MAFK	chr3:19978832-19979814	K562	blood:	n/a	n/a
26	MYC	chr3:19978819-19979565	K562	blood:	n/a	n/a
27	UBTF	chr3:19979192-19979703	K562	blood:	n/a	n/a
28	TRIM28	chr3:19978840-19979600	K562	blood:	n/a	n/a
29	CEBPB	chr3:19979078-19979490	K562	blood:	n/a	n/a
30	GATA2	chr3:19978881-19979525	K562	blood:	n/a	chr3:19979180-19979190 chr3:19979214-19979223 chr3:19979211-19979220 chr3:19979071-19979082 chr3:19979075-19979084 chr3:19979221-19979237
31	EP300	chr3:19978856-19979898	K562	blood:	n/a	chr3:19979176-19979190
32	NR2F2	chr3:19978600-19979692	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:19979101..19981901-chr3:20077826..20080437,2	K562	blood:
2	chr3:19976162..19983592-chr3:19985528..19991017,8	MCF-7	breast:
3	chr3:19979250..19980946-chr3:19981520..19983771,2	K562	blood:
4	chr3:19975673..19977428-chr3:19977475..19979847,2	K562	blood:

Variant related genes	Relation type
EFHB	TF binding region
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12638170	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2171275	0.85[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs2364515	0.82[CHD][hapmap]
rs2929318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929319	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929343	0.85[CHD][hapmap]
rs2929345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929350	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929351	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2929353	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2929354	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929355	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929356	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929357	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929359	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs2929364	0.86[EUR][1000 genomes]
rs2929366	0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs2931400	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2931401	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2931403	0.80[JPT][hapmap]
rs2931407	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57808479	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6550227	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6770750	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792678	0.86[EUR][1000 genomes]
rs7356115	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2929346	SGOL1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19973600-19987200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr3:19975600-19987400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:19976000-19987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:19978400-19979800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:19978600-19979800	Enhancers	NH-A	brain
6	chr3:19978800-19979600	Enhancers	Stomach Mucosa	stomach
7	chr3:19978800-19979600	Flanking Active TSS	K562	blood
8	chr3:19978800-19979800	Enhancers	Osteobl	bone
9	chr3:19979000-19979600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:19979000-19979600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:19979000-19979600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:19979200-19979600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:19979200-19979800	Enhancers	Hela-S3	cervix
14	chr3:19979200-19980000	Enhancers	HepG2	liver
15	chr3:19979400-19979800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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