Variant report

Variant	rs6463551
Chromosome Location	chr7:6389839-6389840
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	SPI1	chr7:6389642-6390106	GM12891	blood:	n/a	chr7:6389855-6389868 chr7:6389856-6389869
2	SPI1	chr7:6389521-6390125	GM12878	blood:	n/a	chr7:6389855-6389868 chr7:6389856-6389869
3	CTCF	chr7:6389760-6389910	HVMF	connective:	n/a	n/a
4	ZNF384	chr7:6389607-6390002	GM12878	blood:	n/a	n/a
5	SPI1	chr7:6389679-6390186	HL-60	blood:	n/a	chr7:6389855-6389868 chr7:6389856-6389869
6	MAX	chr7:6389754-6390533	NB4	blood:	n/a	chr7:6389922-6389932
7	SPI1	chr7:6389691-6389973	GM12891	blood:	n/a	chr7:6389855-6389868 chr7:6389856-6389869
8	SPI1	chr7:6389708-6389996	GM12878	blood:	n/a	chr7:6389855-6389868 chr7:6389856-6389869
9	SPI1	chr7:6389777-6389937	K562	blood:	n/a	chr7:6389855-6389868 chr7:6389856-6389869
10	POLR2A	chr7:6389687-6390517	Raji	blood:	n/a	n/a
11	SPI1	chr7:6389736-6389982	GM12878	blood:	n/a	chr7:6389855-6389868 chr7:6389856-6389869
12	MYC	chr7:6389744-6390659	NB4	blood:	n/a	chr7:6389922-6389932
13	SPI1	chr7:6389604-6390076	HL-60	blood:	n/a	chr7:6389855-6389868 chr7:6389856-6389869

No.	Distal block	Cell Line	Cell type
1	chr7:6046534..6048837-chr7:6387102..6390061,2	MCF-7	breast:
2	chr7:6047922..6050389-chr7:6388573..6391369,3	K562	blood:
3	chr7:6049082..6051960-chr7:6388689..6390680,2	MCF-7	breast:
4	chr7:6120676..6122302-chr7:6388312..6390000,2	MCF-7	breast:

Variant related genes	Relation type
FAM220A	TF binding region
ENSG00000106305	Chromatin interaction
ENSG00000231704	Chromatin interaction
ENSG00000122512	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10278424	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10281392	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10951980	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11505569	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11505570	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12112106	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13226769	0.82[AFR][1000 genomes]
rs13245396	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2113629	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28817584	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4724798	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs755629	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7791772	0.93[AMR][1000 genomes];0.86[EUR][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
rs6463551	RAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 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	chr7:6389600-6390000	Weak transcription	Adipose Nuclei	Adipose
13	chr7:6389600-6390200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:6389600-6390200	Enhancers	Hela-S3	cervix
15	chr7:6389600-6390400	Enhancers	Fetal Brain Male	brain
16	chr7:6389600-6390600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:6389600-6390600	Enhancers	Liver	Liver
18	chr7:6389800-6390000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr7:6389800-6390200	Enhancers	Fetal Brain Female	brain
20	chr7:6389800-6390200	Enhancers	HepG2	liver
21	chr7:6389800-6390200	Enhancers	NHEK	skin
22	chr7:6389800-6390400	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr7:6389800-6390600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:6389800-6390600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr7:6389800-6390600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr7:6389800-6390800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links