Variant report

Variant	rs4979224
Chromosome Location	chr9:115982278-115982279
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	BCLAF1	chr9:115981212-115982657	GM12878	blood:	n/a	chr9:115981634-115981643
2	POU2F2	chr9:115982184-115982630	GM12878	blood:	n/a	n/a
3	EBF1	chr9:115981369-115982712	GM12878	blood:	n/a	n/a
4	ATF2	chr9:115981374-115982764	GM12878	blood:	n/a	n/a
5	MXI1	chr9:115981145-115984347	GM12878	blood:	n/a	n/a
6	PML	chr9:115981826-115984110	GM12878	blood:	n/a	chr9:115983963-115983971
7	SPI1	chr9:115982153-115982524	GM12891	blood:	n/a	n/a
8	MEF2A	chr9:115982093-115982623	GM12878	blood:	n/a	n/a
9	FOS	chr9:115982222-115982512	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr9:115982237-115982549	MCF10A-Er-Src	breast:	n/a	n/a
11	EP300	chr9:115981398-115982763	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
12	POLR2A	chr9:115981373-115984128	GM12891	blood:	n/a	n/a
13	RCOR1	chr9:115981341-115982668	GM12878	blood:	n/a	n/a
14	RELA	chr9:115982122-115984391	GM18951	blood:	n/a	n/a
15	MAX	chr9:115982245-115982616	K562	blood:	n/a	n/a
16	MTA3	chr9:115982162-115983011	GM12878	blood:	n/a	n/a
17	RUNX3	chr9:115981378-115983926	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:115982266-115982881	GM12878	blood:	n/a	n/a
19	NFATC1	chr9:115981569-115982664	GM12878	blood:	n/a	n/a
20	POLR2A	chr9:115982203-115984095	GM18505	blood:	n/a	n/a
21	BATF	chr9:115982206-115982623	GM12878	blood:	n/a	n/a
22	MXI1	chr9:115981681-115985060	SK-N-SH	brain:	n/a	n/a
23	POU2F2	chr9:115982273-115982616	GM12878	blood:	n/a	n/a
24	MYC	chr9:115981797-115982601	K562	blood:	n/a	n/a
25	EP300	chr9:115982158-115983016	GM12878	blood:	n/a	n/a
26	POU2F2	chr9:115982251-115982500	GM12878	blood:	n/a	n/a
27	MAX	chr9:115981479-115984076	GM12878	blood:	n/a	chr9:115983813-115983823
28	MAX	chr9:115981823-115982464	K562	blood:	n/a	n/a
29	CEBPB	chr9:115982248-115982576	IMR90	lung:	n/a	n/a
30	EP300	chr9:115981321-115983093	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
31	BATF	chr9:115982119-115982632	GM12878	blood:	n/a	n/a
32	NFIC	chr9:115981379-115982852	GM12878	blood:	n/a	n/a
33	RELA	chr9:115982255-115983851	GM19193	blood:	n/a	n/a
34	CHD1	chr9:115981494-115983650	GM12878	blood:	n/a	n/a
35	BHLHE40	chr9:115982127-115984239	GM12878	blood:	n/a	chr9:115984103-115984119
36	FOXM1	chr9:115981374-115982779	GM12878	blood:	n/a	n/a
37	MTA3	chr9:115981314-115984189	GM12878	blood:	n/a	n/a
38	IRF1	chr9:115982050-115982518	K562	blood:	n/a	n/a
39	STAT3	chr9:115981472-115982969	GM12878	blood:	n/a	chr9:115982276-115982284 chr9:115982620-115982627
40	POLR2A	chr9:115981548-115984508	GM12878	blood:	n/a	n/a
41	SPI1	chr9:115982243-115982455	GM12878	blood:	n/a	n/a
42	SP1	chr9:115982127-115982658	GM12878	blood:	n/a	n/a
43	ZNF143	chr9:115982232-115982618	GM12878	blood:	n/a	n/a
44	MAX	chr9:115981549-115984373	NB4	blood:	n/a	chr9:115983813-115983823
45	USF2	chr9:115982222-115982630	GM12878	blood:	n/a	n/a
46	BCLAF1	chr9:115981455-115982653	GM12878	blood:	n/a	chr9:115981634-115981643
47	IKZF1	chr9:115981412-115983767	GM12878	blood:	n/a	chr9:115982053-115982061
48	SPI1	chr9:115982229-115982593	GM12878	blood:	n/a	n/a
49	BCL11A	chr9:115982153-115982635	GM12878	blood:	n/a	n/a
50	MXI1	chr9:115982243-115984838	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
2	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
3	chr9:115968725..115971196-chr9:115981878..115984279,2	MCF-7	breast:
4	chr9:115981081..115983502-chr9:115983537..115987172,3	MCF-7	breast:
5	chr9:115981852..115985156-chr9:116171660..116173942,3	MCF-7	breast:
6	chr9:115982263..115984734-chr9:116036359..116038354,4	MCF-7	breast:
7	chr9:115978706..115980364-chr9:115981064..115982891,2	K562	blood:
8	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
9	chr9:115974346..115976683-chr9:115980205..115982463,2	MCF-7	breast:
10	chr9:115949400..115951556-chr9:115979789..115982738,2	MCF-7	breast:

Variant related genes	Relation type
SLC31A1	TF binding region
ENSG00000176386	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10081797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114381	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10114423	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10116039	0.82[GIH][hapmap]
rs10121845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739389	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739391	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759635	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817460	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817465	0.88[ASW][hapmap];0.87[GIH][hapmap];0.90[YRI][hapmap]
rs10817470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338001	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851623	0.84[CEU][hapmap]
rs7855694	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859189	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4979224	CDC26	cis	cerebellum	SCAN
rs4979224	ZNF618	cis	cerebellum	SCAN
rs4979224	CDC26	cis	parietal	SCAN
rs4979224	SVEP1	cis	parietal	SCAN
rs4979224	PRPF4	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115936800-115982400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:115945600-115982800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:115950600-115982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:115950800-115982800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:115951000-115982800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:115969000-115982400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:115969600-115982400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr9:115969600-115982400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:115970000-115982800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:115972600-115982800	Weak transcription	Gastric	stomach
11	chr9:115973200-115982400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:115973200-115982400	Weak transcription	Spleen	Spleen
13	chr9:115973200-115982600	Weak transcription	Ovary	ovary
14	chr9:115973400-115982400	Weak transcription	Esophagus	oesophagus
15	chr9:115973400-115982400	Weak transcription	Pancreas	Pancrea
16	chr9:115973800-115982400	Weak transcription	Fetal Intestine Small	intestine
17	chr9:115973800-115982800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:115973800-115982800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:115973800-115982800	Weak transcription	Lung	lung
20	chr9:115974000-115982400	Weak transcription	Fetal Intestine Large	intestine
21	chr9:115974000-115982400	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:115974000-115982400	Weak transcription	Placenta	Placenta
23	chr9:115975000-115982400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:115975200-115982400	Weak transcription	Left Ventricle	heart
25	chr9:115977400-115982400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:115980200-115982400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr9:115980200-115982400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr9:115980200-115982800	Enhancers	Primary B cells from peripheral blood	blood
29	chr9:115980800-115982400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr9:115980800-115982400	Enhancers	Brain Angular Gyrus	brain
31	chr9:115980800-115982400	Transcr. at gene 5' and 3'	K562	blood
32	chr9:115980800-115982600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr9:115980800-115982800	Enhancers	Stomach Mucosa	stomach
34	chr9:115981000-115982400	Enhancers	Brain Germinal Matrix	brain
35	chr9:115981200-115983200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr9:115981200-115983400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr9:115981200-115985600	Active TSS	GM12878-XiMat	blood
38	chr9:115981400-115982600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr9:115981400-115982800	Flanking Active TSS	Dnd41	blood
40	chr9:115981400-115983000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:115981400-115983200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr9:115981400-115983400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:115981600-115982400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:115981600-115982400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr9:115981600-115983000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:115981800-115982400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:115981800-115982400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:115981800-115982400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:115981800-115982400	Enhancers	Brain Cingulate Gyrus	brain
50	chr9:115981800-115982400	Enhancers	Colon Smooth Muscle	Colon

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