Variant report

Variant	rs11768546
Chromosome Location	chr7:6390564-6390565
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	chr7:6390462-6390715	HepG2	liver:	n/a	chr7:6390575-6390586
2	ZNF384	chr7:6390422-6390600	GM12878	blood:	n/a	n/a
3	CTCF	chr7:6390420-6390570	HL-60	blood:	n/a	n/a
4	CEBPB	chr7:6390518-6390648	A549	lung:	n/a	chr7:6390575-6390586
5	MYC	chr7:6390113-6390703	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr7:6390531-6390623	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr7:6390288-6390696	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr7:6389744-6390659	NB4	blood:	n/a	chr7:6389922-6389932
9	FOS	chr7:6390532-6390623	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6047922..6050389-chr7:6388573..6391369,3	K562	blood:
2	chr7:6049082..6051960-chr7:6388689..6390680,2	MCF-7	breast:
3	chr7:6390235..6392804-chr7:6397143..6398713,2	K562	blood:

Variant related genes	Relation type
FAM220A	TF binding region
ENSG00000106305	Chromatin interaction
ENSG00000122512	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10951981	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11489415	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11772703	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12113291	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12155260	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13229222	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13229636	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28852438	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34208673	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35028446	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35199276	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35671953	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3885847	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4724795	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62454325	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62454327	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6463550	0.82[AFR][1000 genomes]
rs6948491	0.84[AFR][1000 genomes]
rs9648591	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9648592	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv1025381	chr7:6356704-6409818	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv538716	chr7:6365534-6400845	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	esv3439228	chr7:6389232-6394136	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11768546	RAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6388600-6391200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:6388800-6390600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:6388800-6409400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:6389000-6390600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr7:6389000-6390600	Enhancers	Primary hematopoietic stem cells	blood
6	chr7:6389000-6390600	Enhancers	GM12878-XiMat	blood
7	chr7:6389000-6391200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:6389000-6391600	Enhancers	Primary B cells from peripheral blood	blood
9	chr7:6389000-6391800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:6389000-6401800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr7:6389400-6390600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr7:6389600-6390600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:6389600-6390600	Enhancers	Liver	Liver
14	chr7:6389800-6390600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:6389800-6390600	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr7:6389800-6390600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr7:6389800-6390800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:6390000-6390600	Enhancers	Adipose Nuclei	Adipose
19	chr7:6390200-6390600	Flanking Active TSS	NHEK	skin
20	chr7:6390200-6390800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:6390200-6391200	Weak transcription	Fetal Brain Female	brain
22	chr7:6390200-6393600	Weak transcription	HepG2	liver
23	chr7:6390400-6392200	Enhancers	Primary B cells from cord blood	blood

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