Variant report

Variant	rs3810914
Chromosome Location	chr9:115981721-115981722
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	BCLAF1	chr9:115981212-115982657	GM12878	blood:	n/a	chr9:115981634-115981643
2	EBF1	chr9:115981369-115982712	GM12878	blood:	n/a	n/a
3	ATF2	chr9:115981374-115982764	GM12878	blood:	n/a	n/a
4	MXI1	chr9:115981145-115984347	GM12878	blood:	n/a	n/a
5	EP300	chr9:115981398-115982763	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
6	IRF4	chr9:115981455-115981829	GM12878	blood:	n/a	n/a
7	SPI1	chr9:115981381-115981880	HL-60	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
8	POLR2A	chr9:115981373-115984128	GM12891	blood:	n/a	n/a
9	RCOR1	chr9:115981341-115982668	GM12878	blood:	n/a	n/a
10	SRF	chr9:115981561-115981771	GM12878	blood:	n/a	chr9:115981687-115981705 chr9:115981689-115981702
11	REST	chr9:115981529-115981763	Hela-S3	cervix:	n/a	n/a
12	RUNX3	chr9:115981378-115983926	GM12878	blood:	n/a	n/a
13	NFATC1	chr9:115981569-115982664	GM12878	blood:	n/a	n/a
14	BATF	chr9:115981439-115981805	GM12878	blood:	n/a	chr9:115981724-115981732
15	MXI1	chr9:115981681-115985060	SK-N-SH	brain:	n/a	n/a
16	MEF2A	chr9:115981385-115981907	GM12878	blood:	n/a	n/a
17	MAX	chr9:115981479-115984076	GM12878	blood:	n/a	chr9:115983813-115983823
18	STAT1	chr9:115981718-115981917	GM12878	blood:	n/a	n/a
19	BHLHE40	chr9:115981434-115981876	GM12878	blood:	n/a	n/a
20	BCL11A	chr9:115981417-115981873	GM12878	blood:	n/a	chr9:115981634-115981643
21	SPI1	chr9:115981367-115981896	GM12891	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
22	EP300	chr9:115981321-115983093	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
23	NFIC	chr9:115981379-115982852	GM12878	blood:	n/a	n/a
24	CHD1	chr9:115981494-115983650	GM12878	blood:	n/a	n/a
25	SPI1	chr9:115981324-115982003	HL-60	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
26	FOXM1	chr9:115981374-115982779	GM12878	blood:	n/a	n/a
27	SPI1	chr9:115981514-115981775	K562	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
28	MTA3	chr9:115981314-115984189	GM12878	blood:	n/a	n/a
29	STAT3	chr9:115981472-115982969	GM12878	blood:	n/a	chr9:115982276-115982284 chr9:115982620-115982627
30	POLR2A	chr9:115981548-115984508	GM12878	blood:	n/a	n/a
31	PML	chr9:115981523-115981802	GM12878	blood:	n/a	n/a
32	MAX	chr9:115981549-115984373	NB4	blood:	n/a	chr9:115983813-115983823
33	SPI1	chr9:115981367-115981857	GM12878	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
34	EP300	chr9:115981270-115981910	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
35	SPI1	chr9:115981437-115981827	GM12878	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
36	SPI1	chr9:115981403-115981900	GM12891	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
37	BATF	chr9:115981447-115981779	GM12878	blood:	n/a	chr9:115981724-115981732
38	ELK1	chr9:115981464-115982010	GM12878	blood:	n/a	n/a
39	BCLAF1	chr9:115981455-115982653	GM12878	blood:	n/a	chr9:115981634-115981643
40	IKZF1	chr9:115981412-115983767	GM12878	blood:	n/a	chr9:115982053-115982061
41	NFATC1	chr9:115981364-115981978	GM12878	blood:	n/a	n/a
42	MEF2A	chr9:115981486-115981955	GM12878	blood:	n/a	n/a
43	RUNX3	chr9:115981447-115982660	GM12878	blood:	n/a	n/a
44	ATF2	chr9:115981259-115982696	GM12878	blood:	n/a	n/a
45	SPI1	chr9:115981521-115981755	K562	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
46	NFIC	chr9:115981330-115983832	GM12878	blood:	n/a	n/a
47	TBP	chr9:115981444-115982880	GM12878	blood:	n/a	n/a
48	SPI1	chr9:115981156-115982695	GM12878	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
49	CUX1	chr9:115981397-115982619	GM12878	blood:	n/a	n/a
50	TBL1XR1	chr9:115981424-115984437	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
2	chr9:115981081..115983502-chr9:115983537..115987172,3	MCF-7	breast:
3	chr9:115978706..115980364-chr9:115981064..115982891,2	K562	blood:
4	chr9:115974346..115976683-chr9:115980205..115982463,2	MCF-7	breast:
5	chr9:115979271..115982033-chr9:115982056..115983606,2	MCF-7	breast:
6	chr9:115949400..115951556-chr9:115979789..115982738,2	MCF-7	breast:

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

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10081797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[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]
rs10121845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.93[JPT][hapmap];0.90[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];0.93[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	0.90[YRI][hapmap]
rs10817470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs10981698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[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]
rs4978536	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]
rs4979224	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]
rs4979225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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[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]
rs7851623	0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3810914	PRPF4	cis	Thyroid	GTEx

Chromatin state (count:122 , 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	chr9:115965200-115982000	Weak transcription	Colonic Mucosa	Colon
7	chr9:115965200-115982000	Weak transcription	Fetal Brain Male	brain
8	chr9:115965200-115982200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:115969000-115982400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:115969400-115981800	Weak transcription	HSMM	muscle
11	chr9:115969600-115982400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:115969600-115982400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:115970000-115982800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:115970400-115981800	Weak transcription	NH-A	brain
15	chr9:115970600-115981800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:115971600-115982000	Weak transcription	NHDF-Ad	bronchial
17	chr9:115971800-115982000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:115972600-115981800	Weak transcription	HMEC	breast
19	chr9:115972600-115982800	Weak transcription	Gastric	stomach
20	chr9:115972800-115981800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:115972800-115982000	Weak transcription	HSMMtube	muscle
22	chr9:115973200-115981800	Weak transcription	Fetal Kidney	kidney
23	chr9:115973200-115981800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:115973200-115982000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:115973200-115982000	Weak transcription	A549	lung
26	chr9:115973200-115982400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr9:115973200-115982400	Weak transcription	Spleen	Spleen
28	chr9:115973200-115982600	Weak transcription	Ovary	ovary
29	chr9:115973400-115981800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:115973400-115981800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:115973400-115981800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:115973400-115981800	Weak transcription	Thymus	Thymus
33	chr9:115973400-115981800	Weak transcription	NHLF	lung
34	chr9:115973400-115982000	Weak transcription	Fetal Lung	lung
35	chr9:115973400-115982000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:115973400-115982200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:115973400-115982200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr9:115973400-115982400	Weak transcription	Esophagus	oesophagus
39	chr9:115973400-115982400	Weak transcription	Pancreas	Pancrea
40	chr9:115973800-115981800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:115973800-115981800	Weak transcription	Right Ventricle	heart
42	chr9:115973800-115982000	Weak transcription	Aorta	Aorta
43	chr9:115973800-115982200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:115973800-115982400	Weak transcription	Fetal Intestine Small	intestine
45	chr9:115973800-115982800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:115973800-115982800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:115973800-115982800	Weak transcription	Lung	lung
48	chr9:115974000-115981800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:115974000-115981800	Weak transcription	Fetal Thymus	thymus
50	chr9:115974000-115982000	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links