Variant report

Variant	rs3799373
Chromosome Location	chr6:25929173-25929174
allele	A/C
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	MYBL2	chr6:25928606-25930038	HepG2	liver:	n/a	n/a
2	HDAC2	chr6:25929078-25929650	HepG2	liver:	n/a	chr6:25929188-25929202 chr6:25929244-25929258
3	ARID3A	chr6:25928738-25929715	HepG2	liver:	n/a	n/a
4	RAD21	chr6:25929163-25929769	HepG2	liver:	n/a	n/a
5	FOXA2	chr6:25929163-25929577	HepG2	liver:	n/a	chr6:25929195-25929207
6	FOXA2	chr6:25928396-25929930	HepG2	liver:	n/a	chr6:25929632-25929644 chr6:25929195-25929207
7	TEAD4	chr6:25929013-25929772	HepG2	liver:	n/a	n/a
8	FOXA1	chr6:25928635-25929692	HepG2	liver:	n/a	chr6:25929632-25929644 chr6:25929195-25929207 chr6:25928964-25928979
9	NFIC	chr6:25929146-25930014	HepG2	liver:	n/a	n/a
10	MBD4	chr6:25928799-25930033	HepG2	liver:	n/a	n/a
11	HDAC2	chr6:25929169-25929658	HepG2	liver:	n/a	chr6:25929188-25929202 chr6:25929244-25929258
12	FOXA1	chr6:25928614-25929770	HepG2	liver:	n/a	chr6:25929632-25929644 chr6:25929195-25929207 chr6:25928964-25928979
13	FOXA2	chr6:25928789-25929250	A549	lung:	n/a	chr6:25929195-25929207
14	FOXA1	chr6:25928702-25929695	HepG2	liver:	n/a	chr6:25929632-25929644 chr6:25929195-25929207 chr6:25928964-25928979
15	CEBPB	chr6:25929165-25929544	HepG2	liver:	n/a	n/a
16	EP300	chr6:25928696-25929778	HepG2	liver:	n/a	chr6:25928803-25928817
17	FOXA1	chr6:25928796-25929622	HepG2	liver:	n/a	chr6:25929195-25929207 chr6:25928964-25928979
18	CEBPB	chr6:25929165-25929551	HepG2	liver:	n/a	n/a
19	SP1	chr6:25928696-25929704	HepG2	liver:	n/a	n/a
20	TCF7L2	chr6:25928810-25929746	HepG2	liver:	n/a	n/a
21	ZEB1	chr6:25929152-25929749	HepG2	liver:	n/a	n/a
22	NFIC	chr6:25928628-25929786	HepG2	liver:	n/a	n/a
23	CEBPB	chr6:25929142-25929630	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25922119..25925383-chr6:25927445..25929839,3	K562	blood:
2	chr6:25928747..25930634-chr6:25945597..25948146,2	K562	blood:

Variant related genes	Relation type
SLC17A2	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10946800	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1115920	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1130000	0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12195653	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12209482	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1324084	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1436306	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1436307	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1436308	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1540273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541987	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1816546	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1865760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2008015	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2013063	0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2032450	0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2071297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071300	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2071301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2157050	0.81[CHB][hapmap]
rs2164485	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2164487	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2328903	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2876693	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3752421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3799371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3799372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3830057	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3846838	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3903852	0.81[ASN][1000 genomes]
rs4478388	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56118523	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62394490	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6456705	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6905887	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6910138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6910174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6915834	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6926383	0.89[ASN][1000 genomes]
rs6928951	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6929805	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6932113	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6938233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7450342	0.94[CHB][hapmap]
rs7739966	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7749342	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs7757666	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766342	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7766478	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7770139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295673	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9295674	0.81[ASN][1000 genomes]
rs9295677	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9295679	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9295680	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9295681	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9348697	0.83[ASN][1000 genomes]
rs9348698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9358891	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358892	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9358893	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9358894	0.81[ASN][1000 genomes]
rs9358895	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358896	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9379801	0.87[CHB][hapmap]
rs9379802	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9379806	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9379807	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9379815	0.83[AMR][1000 genomes]
rs9393675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393677	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9393678	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9461224	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461227	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9461229	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9467636	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467641	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9467645	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9467646	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467647	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9467648	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9467650	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9467651	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9467652	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9467656	0.80[CEU][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv5229	chr6:25912151-25956558	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3799373	U91328.19	cis	Muscle Skeletal	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25928200-25930800	Flanking Active TSS	HepG2	liver
2	chr6:25928200-25931000	Active TSS	Liver	Liver
3	chr6:25928400-25934400	Weak transcription	Small Intestine	intestine
4	chr6:25928800-25929600	Enhancers	Fetal Intestine Small	intestine
5	chr6:25928800-25929600	Enhancers	A549	lung
6	chr6:25928800-25929800	Enhancers	Fetal Intestine Large	intestine
7	chr6:25929000-25931600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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