Variant report

Variant	rs7875607
Chromosome Location	chr9:6004719-6004720
allele	C/T
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	FOS	chr9:6004555-6004877	MCF10A-Er-Src	breast:	n/a	chr9:6004708-6004715 chr9:6004849-6004859 chr9:6004850-6004857 chr9:6004705-6004717 chr9:6004849-6004859 chr9:6004706-6004715 chr9:6004707-6004716 chr9:6004850-6004858 chr9:6004706-6004716 chr9:6004581-6004590 chr9:6004707-6004715 chr9:6004850-6004858
2	FOS	chr9:6004574-6004892	MCF10A-Er-Src	breast:	n/a	chr9:6004708-6004715 chr9:6004849-6004859 chr9:6004850-6004857 chr9:6004705-6004717 chr9:6004849-6004859 chr9:6004706-6004715 chr9:6004707-6004716 chr9:6004850-6004858 chr9:6004706-6004716 chr9:6004581-6004590 chr9:6004707-6004715 chr9:6004850-6004858
3	JUN	chr9:6004595-6004814	HepG2	liver:	n/a	chr9:6004708-6004715 chr9:6004705-6004717 chr9:6004706-6004715 chr9:6004707-6004716 chr9:6004706-6004716 chr9:6004707-6004715
4	JUND	chr9:6004545-6004864	HepG2	liver:	n/a	chr9:6004708-6004715 chr9:6004849-6004859 chr9:6004850-6004857 chr9:6004705-6004717 chr9:6004849-6004859 chr9:6004706-6004715 chr9:6004705-6004716 chr9:6004707-6004716 chr9:6004850-6004858 chr9:6004706-6004716 chr9:6004581-6004590 chr9:6004707-6004715 chr9:6004850-6004858
5	FOS	chr9:6004550-6004894	MCF10A-Er-Src	breast:	n/a	chr9:6004708-6004715 chr9:6004849-6004859 chr9:6004850-6004857 chr9:6004705-6004717 chr9:6004849-6004859 chr9:6004706-6004715 chr9:6004707-6004716 chr9:6004850-6004858 chr9:6004706-6004716 chr9:6004581-6004590 chr9:6004707-6004715 chr9:6004850-6004858
6	FOS	chr9:6004519-6004877	MCF10A-Er-Src	breast:	n/a	chr9:6004708-6004715 chr9:6004849-6004859 chr9:6004850-6004857 chr9:6004705-6004717 chr9:6004849-6004859 chr9:6004706-6004715 chr9:6004707-6004716 chr9:6004850-6004858 chr9:6004706-6004716 chr9:6004581-6004590 chr9:6004707-6004715 chr9:6004850-6004858

No.	Distal block	Cell Line	Cell type
1	chr9:5994344..5996222-chr9:6002760..6005838,3	K562	blood:
2	chr9:5957297..5958890-chr9:6003924..6006485,2	K562	blood:
3	chr9:6004555..6006202-chr9:6015044..6016975,2	MCF-7	breast:
4	chr9:5979666..5981204-chr9:6003336..6005600,2	K562	blood:

Variant related genes	Relation type
MIR4665	TF binding region
ENSG00000137040	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10116214	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975350	1.00[EUR][1000 genomes]
rs10975351	1.00[EUR][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975372	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975377	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	0.91[AMR][1000 genomes]
rs12337300	1.00[EUR][1000 genomes]
rs12337445	1.00[EUR][1000 genomes]
rs12337790	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339713	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339886	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339889	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340153	1.00[EUR][1000 genomes]
rs12340531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341021	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342166	1.00[EUR][1000 genomes]
rs12342282	1.00[EUR][1000 genomes]
rs12343325	1.00[EUR][1000 genomes]
rs12345849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351533	1.00[EUR][1000 genomes]
rs12352918	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1411949	1.00[EUR][1000 genomes]
rs1993912	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28431078	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs386775	1.00[EUR][1000 genomes]
rs57154492	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58291302	1.00[EUR][1000 genomes]
rs60037728	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes]
rs7029847	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383109	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383113	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383114	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383144	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73385128	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73387085	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73389036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397307	1.00[EUR][1000 genomes]
rs73397376	1.00[EUR][1000 genomes]
rs73399307	1.00[EUR][1000 genomes]
rs73639554	1.00[EUR][1000 genomes]
rs73639568	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853706	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7854980	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299025	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5940000-6006800	Weak transcription	Gastric	stomach
2	chr9:5948000-6006000	Weak transcription	Right Ventricle	heart
3	chr9:5950600-6006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:5967200-6006000	Weak transcription	Colonic Mucosa	Colon
5	chr9:5968400-6005600	Weak transcription	Fetal Kidney	kidney
6	chr9:5972200-6005800	Weak transcription	NH-A	brain
7	chr9:5974000-6006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:5975200-6005800	Weak transcription	Fetal Stomach	stomach
9	chr9:5977400-6004800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr9:5977400-6005600	Weak transcription	NHLF	lung
11	chr9:5977400-6005800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:5977400-6006800	Weak transcription	Pancreas	Pancrea
13	chr9:5977400-6007000	Weak transcription	Spleen	Spleen
14	chr9:5982800-6005200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:5987200-6005200	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:5987200-6006200	Weak transcription	Thymus	Thymus
17	chr9:5988000-6005600	Weak transcription	Adipose Nuclei	Adipose
18	chr9:5988000-6005600	Weak transcription	Fetal Lung	lung
19	chr9:5988000-6006200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:5988200-6005600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:5988200-6005800	Weak transcription	HSMM	muscle
22	chr9:5988200-6006000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr9:5988600-6004800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:5988600-6005800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr9:5988800-6005600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:5989000-6006600	Weak transcription	Placenta	Placenta
27	chr9:5990200-6005400	Weak transcription	Fetal Intestine Small	intestine
28	chr9:5991800-6006800	Weak transcription	Esophagus	oesophagus
29	chr9:5994000-6005200	Weak transcription	Left Ventricle	heart
30	chr9:5997200-6005800	Weak transcription	Stomach Mucosa	stomach
31	chr9:5997200-6006000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:5997200-6006000	Weak transcription	Right Atrium	heart
33	chr9:5997400-6006200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:5997800-6005800	Weak transcription	Ovary	ovary
35	chr9:5998000-6004800	Weak transcription	NHEK	skin
36	chr9:5998000-6005800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:5999600-6007000	Weak transcription	Lung	lung
38	chr9:5999800-6006000	Weak transcription	Brain Substantia Nigra	brain
39	chr9:6000000-6005200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:6000000-6005400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:6000000-6005600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:6001200-6005200	Weak transcription	Small Intestine	intestine
43	chr9:6001400-6005600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:6001400-6005800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:6001400-6006200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:6001600-6005200	Weak transcription	Psoas Muscle	Psoas
47	chr9:6001600-6005600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:6001600-6006000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:6001800-6005400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr9:6002200-6004800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links