Variant report

Variant	rs783404
Chromosome Location	chr6:106956896-106956897
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	CEBPB	chr6:106956719-106957068	HepG2	liver:	n/a	chr6:106956882-106956893
2	FOS	chr6:106956732-106957113	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr6:106956817-106956974	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr6:106956709-106957119	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr6:106956745-106957051	MCF-7	breast:	n/a	chr6:106956882-106956893
6	E2F4	chr6:106956826-106957360	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr6:106956731-106957021	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr6:106956796-106957116	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr6:106956710-106957069	Hela-S3	cervix:	n/a	chr6:106956882-106956893
10	MYC	chr6:106956676-106957071	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr6:106956709-106957159	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr6:106956707-106957072	IMR90	lung:	n/a	chr6:106956882-106956893
13	FOS	chr6:106956711-106957154	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr6:106956735-106957088	K562	blood:	n/a	chr6:106956882-106956893
15	STAT3	chr6:106956795-106957029	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr6:106956727-106956918	H1-hESC	embryonic stem cell:	n/a	chr6:106956882-106956893
17	POLR2A	chr6:106956874-106957027	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr6:106956775-106957014	A549	lung:	n/a	chr6:106956882-106956893
19	POLR2A	chr6:106956819-106957123	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr6:106956750-106957093	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:106955204..106959628-chr6:106966256..106969365,4	K562	blood:
2	chr6:106956358..106959318-chr6:106991274..106994095,2	MCF-7	breast:
3	chr6:106937827..106940200-chr6:106954581..106957012,2	K562	blood:

Variant related genes	Relation type
AIM1	TF binding region
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs710096	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs710097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs783407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783417	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs783420	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783422	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783423	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936497	0.88[CHB][hapmap];1.00[JPT][hapmap]

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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1025510	chr6:106791080-106982400	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538404	chr6:106791080-106982400	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs783404	EEF1A2	trans	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106945600-106957600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:106950000-106957800	Weak transcription	Pancreas	Pancrea
3	chr6:106951200-106957400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:106951400-106957800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:106951600-106957000	Weak transcription	NHEK	skin
6	chr6:106952600-106957600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:106955400-106957400	Weak transcription	Esophagus	oesophagus
8	chr6:106955600-106957400	Weak transcription	HMEC	breast
9	chr6:106956400-106957600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:106956400-106957600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:106956600-106957200	Enhancers	Hela-S3	cervix
12	chr6:106956600-106957400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:106956600-106957400	Enhancers	Adipose Nuclei	Adipose
14	chr6:106956600-106957600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr6:106956600-106958000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:106956800-106957000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr6:106956800-106957000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:106956800-106957000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:106956800-106957000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:106956800-106957000	Enhancers	Dnd41	blood
21	chr6:106956800-106957200	Enhancers	Primary B cells from cord blood	blood
22	chr6:106956800-106957200	Enhancers	Primary hematopoietic stem cells	blood
23	chr6:106956800-106957800	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr6:106956800-106957800	Bivalent Enhancer	NHLF	lung
25	chr6:106956800-106959600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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