Variant report

Variant	rs3810915
Chromosome Location	chr9:115981771-115981772
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	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	RUNX3	chr9:115981378-115983926	GM12878	blood:	n/a	n/a
12	NFATC1	chr9:115981569-115982664	GM12878	blood:	n/a	n/a
13	BATF	chr9:115981439-115981805	GM12878	blood:	n/a	chr9:115981724-115981732
14	MXI1	chr9:115981681-115985060	SK-N-SH	brain:	n/a	n/a
15	MEF2A	chr9:115981385-115981907	GM12878	blood:	n/a	n/a
16	MAX	chr9:115981479-115984076	GM12878	blood:	n/a	chr9:115983813-115983823
17	STAT1	chr9:115981718-115981917	GM12878	blood:	n/a	n/a
18	BHLHE40	chr9:115981434-115981876	GM12878	blood:	n/a	n/a
19	BCL11A	chr9:115981417-115981873	GM12878	blood:	n/a	chr9:115981634-115981643
20	SPI1	chr9:115981367-115981896	GM12891	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
21	EP300	chr9:115981321-115983093	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
22	NFIC	chr9:115981379-115982852	GM12878	blood:	n/a	n/a
23	CHD1	chr9:115981494-115983650	GM12878	blood:	n/a	n/a
24	SPI1	chr9:115981324-115982003	HL-60	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
25	FOXM1	chr9:115981374-115982779	GM12878	blood:	n/a	n/a
26	SPI1	chr9:115981514-115981775	K562	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
27	MTA3	chr9:115981314-115984189	GM12878	blood:	n/a	n/a
28	STAT3	chr9:115981472-115982969	GM12878	blood:	n/a	chr9:115982276-115982284 chr9:115982620-115982627
29	POLR2A	chr9:115981548-115984508	GM12878	blood:	n/a	n/a
30	PML	chr9:115981523-115981802	GM12878	blood:	n/a	n/a
31	MAX	chr9:115981549-115984373	NB4	blood:	n/a	chr9:115983813-115983823
32	SPI1	chr9:115981367-115981857	GM12878	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
33	EP300	chr9:115981270-115981910	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
34	SPI1	chr9:115981437-115981827	GM12878	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
35	SPI1	chr9:115981403-115981900	GM12891	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
36	BATF	chr9:115981447-115981779	GM12878	blood:	n/a	chr9:115981724-115981732
37	ELK1	chr9:115981464-115982010	GM12878	blood:	n/a	n/a
38	BCLAF1	chr9:115981455-115982653	GM12878	blood:	n/a	chr9:115981634-115981643
39	IKZF1	chr9:115981412-115983767	GM12878	blood:	n/a	chr9:115982053-115982061
40	NFATC1	chr9:115981364-115981978	GM12878	blood:	n/a	n/a
41	MEF2A	chr9:115981486-115981955	GM12878	blood:	n/a	n/a
42	RUNX3	chr9:115981447-115982660	GM12878	blood:	n/a	n/a
43	ATF2	chr9:115981259-115982696	GM12878	blood:	n/a	n/a
44	NFIC	chr9:115981330-115983832	GM12878	blood:	n/a	n/a
45	TBP	chr9:115981444-115982880	GM12878	blood:	n/a	n/a
46	SPI1	chr9:115981156-115982695	GM12878	blood:	n/a	chr9:115981631-115981638 chr9:115981627-115981640 chr9:115981628-115981641 chr9:115981630-115981639 chr9:115981634-115981643
47	CUX1	chr9:115981397-115982619	GM12878	blood:	n/a	n/a
48	TBL1XR1	chr9:115981424-115984437	GM12878	blood:	n/a	n/a
49	IRF4	chr9:115981407-115982573	GM12878	blood:	n/a	n/a
50	STAT5A	chr9:115981384-115982667	GM12878	blood:	n/a	chr9:115982276-115982284 chr9:115982620-115982627

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	chr9:115981081..115983502-chr9:115983537..115987172,3	MCF-7	breast:
4	chr9:115978706..115980364-chr9:115981064..115982891,2	K562	blood:
5	chr9:115974346..115976683-chr9:115980205..115982463,2	MCF-7	breast:
6	chr9:115979271..115982033-chr9:115982056..115983606,2	MCF-7	breast:
7	chr9:115949400..115951556-chr9:115979789..115982738,2	MCF-7	breast:

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

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10817477	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs10981711	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AFR][1000 genomes]
rs10981713	1.00[CEU][hapmap]
rs10981714	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[AFR][1000 genomes]
rs10981719	1.00[CEU][hapmap]
rs10981725	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs10981734	1.00[CEU][hapmap]
rs10981736	1.00[CEU][hapmap]
rs12684385	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs12982	0.82[CEU][hapmap]
rs16926630	0.82[CEU][hapmap]
rs16930959	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16931182	1.00[EUR][1000 genomes]
rs16932083	0.83[AFR][1000 genomes]
rs16932730	1.00[CEU][hapmap]
rs16932806	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs2296074	1.00[ASW][hapmap]
rs2296075	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs2296076	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs2418249	1.00[CEU][hapmap]
rs3810920	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs4355846	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4641140	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58039219	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59987461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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
rs3810915	WDR31	cis	lymphoblastoid	seeQTL

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

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