Variant report

Variant	rs680729
Chromosome Location	chr9:79322720-79322721
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	FOXM1	chr9:79322377-79322869	GM12878	blood:	n/a	n/a
2	RUNX3	chr9:79322356-79322854	GM12878	blood:	n/a	n/a
3	NFATC1	chr9:79322357-79322829	GM12878	blood:	n/a	n/a
4	MEF2A	chr9:79322331-79322797	GM12878	blood:	n/a	n/a
5	MEF2C	chr9:79322364-79322892	GM12878	blood:	n/a	chr9:79322625-79322640
6	NFIC	chr9:79322280-79322981	GM12878	blood:	n/a	n/a
7	RUNX3	chr9:79322437-79322804	GM12878	blood:	n/a	n/a
8	MEF2A	chr9:79322336-79322817	GM12878	blood:	n/a	n/a
9	ATF2	chr9:79322453-79322794	GM12878	blood:	n/a	n/a
10	NFATC1	chr9:79322280-79322908	GM12878	blood:	n/a	n/a
11	POU2F2	chr9:79322400-79322817	GM12891	blood:	n/a	n/a
12	BCL11A	chr9:79322459-79322843	GM12878	blood:	n/a	n/a
13	POU2F2	chr9:79322444-79322806	GM12891	blood:	n/a	n/a
14	CREB1	chr9:79322355-79322925	GM12878	blood:	n/a	n/a
15	BATF	chr9:79322377-79322785	GM12878	blood:	n/a	chr9:79322530-79322541
16	ATF2	chr9:79322288-79322922	GM12878	blood:	n/a	n/a
17	CREB1	chr9:79322427-79322941	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:79077933..79079433-chr9:79321608..79323340,2	K562	blood:
2	chr9:79213561..79216371-chr9:79320656..79323527,2	MCF-7	breast:
3	chr9:79321119..79322904-chr9:79325137..79328012,2	MCF-7	breast:
4	chr9:79296367..79298472-chr9:79320957..79323696,2	MCF-7	breast:
5	chr9:79073827..79075700-chr9:79322081..79324440,2	MCF-7	breast:

Variant related genes	Relation type
PRUNE2	TF binding region
ENSG00000106772	Chromatin interaction
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10869799	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500952	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505034	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs506086	0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs509489	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs512110	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517634	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554143	0.82[EUR][1000 genomes]
rs556725	0.88[CEU][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs560094	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561970	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566584	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572737	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591411	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594498	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594586	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611461	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615187	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs618145	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620321	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620476	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620552	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620737	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625981	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs626416	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs646698	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650682	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs677913	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs678943	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs680775	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018971	0.82[EUR][1000 genomes]
rs7033337	0.86[EUR][1000 genomes]
rs7033978	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv2754389	chr9:79318677-79333056	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs680729	FAM108B1	cis	parietal	SCAN
rs680729	PRUNE2	cis	Whole Blood	GTEx
rs680729	C9orf85	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79315200-79327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:79316200-79330800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:79316600-79324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:79316800-79322800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:79316800-79325400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:79317400-79327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:79317400-79328600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:79317600-79330800	Strong transcription	HSMM	muscle
13	chr9:79317800-79328600	Strong transcription	HSMMtube	muscle
14	chr9:79318000-79330400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:79318400-79330000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:79318800-79323200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:79320000-79322800	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:79320000-79328000	Strong transcription	Aorta	Aorta
19	chr9:79320000-79328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:79320000-79331200	Weak transcription	Brain Anterior Caudate	brain
21	chr9:79320000-79332000	Weak transcription	Brain Angular Gyrus	brain
22	chr9:79320200-79323200	Weak transcription	Brain Substantia Nigra	brain
23	chr9:79320400-79328600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr9:79321800-79324600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:79322000-79324600	Weak transcription	Colonic Mucosa	Colon
26	chr9:79322200-79324200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr9:79322400-79327000	Strong transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links