Variant report

Variant	rs1323470
Chromosome Location	chr9:102130758-102130759
allele	G/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	MEF2A	chr9:102130399-102131134	GM12878	blood:	n/a	chr9:102130743-102130758 chr9:102130746-102130757 chr9:102130744-102130759 chr9:102130744-102130759 chr9:102130739-102130760 chr9:102130744-102130758 chr9:102130745-102130756 chr9:102130739-102130760 chr9:102130743-102130759 chr9:102130746-102130755
2	PML	chr9:102130417-102131053	GM12878	blood:	n/a	chr9:102130886-102130894
3	BCL3	chr9:102130588-102130936	GM12878	blood:	n/a	n/a
4	RUNX3	chr9:102130504-102130985	GM12878	blood:	n/a	n/a
5	CUX1	chr9:102130688-102130801	GM12878	blood:	n/a	n/a
6	FOXM1	chr9:102130429-102131095	GM12878	blood:	n/a	n/a
7	RAD21	chr9:102130631-102131197	IMR90	lung:	n/a	n/a
8	CREB1	chr9:102130503-102131021	GM12878	blood:	n/a	n/a
9	STAT1	chr9:102130616-102130811	GM12878	blood:	n/a	n/a
10	SP1	chr9:102130589-102130923	GM12878	blood:	n/a	n/a
11	FOXM1	chr9:102130435-102131045	GM12878	blood:	n/a	n/a
12	EBF1	chr9:102130604-102130958	GM12878	blood:	n/a	n/a
13	ATF2	chr9:102130458-102131029	GM12878	blood:	n/a	n/a
14	EP300	chr9:102130565-102130926	GM12878	blood:	n/a	n/a
15	RCOR1	chr9:102130567-102131006	GM12878	blood:	n/a	n/a
16	MEF2C	chr9:102130446-102131154	GM12878	blood:	n/a	chr9:102130743-102130758 chr9:102130746-102130757 chr9:102130744-102130759 chr9:102130744-102130759 chr9:102130739-102130760 chr9:102130744-102130758 chr9:102130745-102130756 chr9:102130739-102130760 chr9:102130743-102130759 chr9:102130746-102130755
17	POU2F2	chr9:102130544-102130942	GM12878	blood:	n/a	chr9:102130814-102130826
18	CHD2	chr9:102130502-102130962	GM12878	blood:	n/a	n/a
19	CTCF	chr9:102130640-102130790	GM12873	blood:	n/a	n/a
20	PAX5	chr9:102130453-102131047	GM12878	blood:	n/a	n/a
21	EGR1	chr9:102130621-102130895	GM12878	blood:	n/a	n/a
22	EP300	chr9:102130523-102130968	GM12878	blood:	n/a	n/a
23	MXI1	chr9:102130529-102130867	GM12878	blood:	n/a	n/a
24	POU2F2	chr9:102130564-102130944	GM12891	blood:	n/a	chr9:102130814-102130826
25	CEBPB	chr9:102130446-102131008	GM12878	blood:	n/a	n/a
26	EP300	chr9:102130574-102131100	GM12878	blood:	n/a	n/a
27	BCL11A	chr9:102130572-102130975	GM12878	blood:	n/a	n/a
28	NFATC1	chr9:102130544-102130874	GM12878	blood:	n/a	n/a
29	BCLAF1	chr9:102130497-102130953	GM12878	blood:	n/a	n/a
30	MAZ	chr9:102130438-102131307	IMR90	lung:	n/a	chr9:102130468-102130479 chr9:102130469-102130478 chr9:102130469-102130479 chr9:102130467-102130480 chr9:102130469-102130478 chr9:102130922-102130932 chr9:102130470-102130477
31	SP1	chr9:102130575-102131009	GM12878	blood:	n/a	n/a
32	BCL11A	chr9:102130573-102130874	GM12878	blood:	n/a	n/a
33	NFIC	chr9:102130465-102130997	GM12878	blood:	n/a	n/a
34	MTA3	chr9:102130553-102130957	GM12878	blood:	n/a	n/a
35	ELK1	chr9:102130663-102130855	GM12878	blood:	n/a	n/a
36	USF2	chr9:102130636-102130860	GM12878	blood:	n/a	n/a
37	STAT3	chr9:102130626-102130850	GM12878	blood:	n/a	n/a
38	POU2F2	chr9:102130469-102130962	GM12878	blood:	n/a	chr9:102130814-102130826
39	MAX	chr9:102130653-102130853	GM12878	blood:	n/a	n/a
40	ATF2	chr9:102130479-102131020	GM12878	blood:	n/a	n/a
41	BATF	chr9:102130604-102130891	GM12878	blood:	n/a	n/a
42	IKZF1	chr9:102130637-102131007	GM12878	blood:	n/a	n/a
43	NFATC1	chr9:102130509-102130938	GM12878	blood:	n/a	n/a
44	MTA3	chr9:102130472-102131000	GM12878	blood:	n/a	n/a
45	NFIC	chr9:102130505-102131094	GM12878	blood:	n/a	n/a
46	BHLHE40	chr9:102130532-102130978	GM12878	blood:	n/a	chr9:102130852-102130868
47	SMC3	chr9:102130549-102130830	GM12878	blood:	n/a	n/a
48	EBF1	chr9:102130535-102131081	GM12878	blood:	n/a	n/a
49	MEF2C	chr9:102130507-102130951	GM12878	blood:	n/a	chr9:102130743-102130758 chr9:102130746-102130757 chr9:102130744-102130759 chr9:102130744-102130759 chr9:102130739-102130760 chr9:102130744-102130758 chr9:102130745-102130756 chr9:102130739-102130760 chr9:102130743-102130759 chr9:102130746-102130755
50	STAT5A	chr9:102130532-102130925	GM12878	blood:	n/a	chr9:102130867-102130879

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102129944..102132650-chr9:102133086..102135348,2	MCF-7	breast:

Variant related genes	Relation type
NAMA	TF binding region
ENSG00000271086	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10491654	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739780	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10760680	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819657	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555572	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555573	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1626179	0.86[ASN][1000 genomes]
rs1648636	0.84[ASN][1000 genomes]
rs16918536	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170461	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1746153	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs192965	0.86[ASN][1000 genomes]
rs2281728	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586563	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs323723	0.89[ASN][1000 genomes]
rs323724	0.88[ASN][1000 genomes]
rs323725	0.89[ASN][1000 genomes]
rs323726	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs323734	0.89[ASN][1000 genomes]
rs323735	0.89[ASN][1000 genomes]
rs398150	0.89[ASN][1000 genomes]
rs398676	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs417512	0.89[ASN][1000 genomes]
rs439733	0.89[ASN][1000 genomes]
rs4742768	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs696875	0.89[ASN][1000 genomes]
rs696876	0.89[ASN][1000 genomes]
rs701343	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs701344	0.89[ASN][1000 genomes]
rs701347	0.89[ASN][1000 genomes]
rs701349	0.89[ASN][1000 genomes]
rs701350	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7023945	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7024065	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029079	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7030379	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7037489	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038667	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7871334	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs988245	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893620	chr9:102029791-102194921	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv831667	chr9:102068047-102285691	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1046898	chr9:102111890-102163313	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102114800-102131600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:102126600-102131000	Enhancers	Fetal Heart	heart
3	chr9:102128200-102130800	Weak transcription	HMEC	breast
4	chr9:102128600-102130800	Enhancers	Psoas Muscle	Psoas
5	chr9:102128800-102130800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:102129400-102131600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:102129800-102130800	Enhancers	Left Ventricle	heart
8	chr9:102129800-102132000	Enhancers	Fetal Brain Male	brain
9	chr9:102130200-102130800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr9:102130200-102130800	Flanking Active TSS	Brain Substantia Nigra	brain
11	chr9:102130200-102130800	Bivalent Enhancer	Fetal Thymus	thymus
12	chr9:102130200-102130800	Enhancers	Spleen	Spleen
13	chr9:102130200-102131000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr9:102130200-102131400	Flanking Active TSS	NHDF-Ad	bronchial
15	chr9:102130400-102130800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
16	chr9:102130400-102130800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:102130400-102130800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:102130400-102130800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
19	chr9:102130400-102130800	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr9:102130400-102130800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:102130400-102130800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr9:102130400-102130800	Bivalent Enhancer	Fetal Intestine Large	intestine
23	chr9:102130400-102130800	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr9:102130400-102131000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:102130400-102131200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr9:102130400-102131200	Flanking Active TSS	Fetal Brain Female	brain
27	chr9:102130400-102131200	Flanking Active TSS	GM12878-XiMat	blood
28	chr9:102130400-102131200	Flanking Active TSS	HSMM	muscle
29	chr9:102130400-102131200	Flanking Active TSS	HUVEC	blood vessel
30	chr9:102130400-102131400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:102130400-102131400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:102130400-102131400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:102130400-102131400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr9:102130400-102131400	Active TSS	Brain Germinal Matrix	brain
35	chr9:102130400-102131400	Flanking Active TSS	NH-A	brain
36	chr9:102130400-102131400	Flanking Active TSS	Osteobl	bone
37	chr9:102130400-102131600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:102130400-102131600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:102130400-102131600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:102130400-102131600	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr9:102130400-102132000	Enhancers	Pancreas	Pancrea
42	chr9:102130400-102132200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr9:102130600-102130800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr9:102130600-102130800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr9:102130600-102130800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
46	chr9:102130600-102130800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:102130600-102130800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:102130600-102130800	Enhancers	Esophagus	oesophagus
49	chr9:102130600-102130800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr9:102130600-102130800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine

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