Variant report

Variant	rs9609296
Chromosome Location	chr22:31891784-31891785
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	MAZ	chr22:31891683-31892958	GM12878	blood:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
2	TBP	chr22:31891781-31892634	Hela-S3	cervix:	n/a	chr22:31892246-31892257
3	POLR2A	chr22:31891653-31892770	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr22:31891648-31892911	U87	brain:	n/a	n/a
5	POLR2A	chr22:31891678-31893258	GM18505	blood:	n/a	n/a
6	MAX	chr22:31891775-31893208	A549	lung:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
7	POLR2A	chr22:31891774-31892797	SK-N-SH	brain:	n/a	n/a
8	MXI1	chr22:31891626-31893666	GM12878	blood:	n/a	n/a
9	MYC	chr22:31891715-31892809	K562	blood:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
10	POLR2A	chr22:31891709-31892903	SK-N-MC	brain:	n/a	n/a
11	CHD1	chr22:31891718-31893077	GM12878	blood:	n/a	n/a
12	POLR2A	chr22:31891765-31893584	GM12878	blood:	n/a	n/a
13	ELF1	chr22:31891688-31892716	MCF-7	breast:	n/a	chr22:31891733-31891744 chr22:31892120-31892131
14	PML	chr22:31891297-31893892	GM12878	blood:	n/a	n/a
15	MXI1	chr22:31891659-31893366	IMR90	lung:	n/a	n/a
16	STAT5A	chr22:31891611-31892424	GM12878	blood:	n/a	n/a
17	POLR2A	chr22:31891612-31893621	GM12878	blood:	n/a	n/a
18	BHLHE40	chr22:31891722-31892771	GM12878	blood:	n/a	n/a
19	POLR2A	chr22:31891648-31892905	U87	brain:	n/a	n/a
20	MYC	chr22:31891758-31893281	NB4	blood:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
21	MAX	chr22:31891777-31893435	NB4	blood:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
22	NFIC	chr22:31891772-31892416	GM12878	blood:	n/a	n/a
23	POLR2A	chr22:31891782-31893149	GM19099	blood:	n/a	n/a
24	NFIC	chr22:31891437-31892817	GM12878	blood:	n/a	n/a
25	EP300	chr22:31891635-31892517	GM12878	blood:	n/a	chr22:31892195-31892204 chr22:31892123-31892130
26	MAZ	chr22:31891562-31893155	IMR90	lung:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
27	GABPA	chr22:31891724-31893017	MCF-7	breast:	n/a	chr22:31892195-31892204
28	POLR2A	chr22:31891505-31893529	GM12891	blood:	n/a	n/a
29	BRCA1	chr22:31891700-31891929	Hela-S3	cervix:	n/a	n/a
30	MTA3	chr22:31891303-31893982	GM12878	blood:	n/a	n/a
31	STAT5A	chr22:31891671-31893344	GM12878	blood:	n/a	chr22:31892843-31892855
32	CHD1	chr22:31891777-31892041	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr22:31891767-31893207	PBDE	blood:	n/a	n/a
34	TBP	chr22:31891752-31892699	GM12878	blood:	n/a	chr22:31892246-31892257
35	EBF1	chr22:31891676-31892585	GM12878	blood:	n/a	n/a
36	POLR2A	chr22:31891767-31893518	GM12878	blood:	n/a	n/a
37	MYC	chr22:31891670-31893077	K562	blood:	n/a	chr22:31891799-31891810 chr22:31891799-31891810
38	POLR2A	chr22:31891573-31892868	MCF10A-Er-Src	breast:	n/a	n/a
39	RELA	chr22:31891750-31892706	GM18505	blood:	n/a	n/a
40	MXI1	chr22:31891400-31893326	SK-N-SH	brain:	n/a	n/a
41	BHLHE40	chr22:31891655-31892707	K562	blood:	n/a	n/a
42	ELF1	chr22:31891766-31893196	GM12878	blood:	n/a	chr22:31892120-31892131
43	FOXM1	chr22:31891763-31892728	GM12878	blood:	n/a	n/a
44	RCOR1	chr22:31891679-31893457	GM12878	blood:	n/a	n/a
45	TBL1XR1	chr22:31891716-31892752	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31891360..31893218-chr22:32058204..32060412,2	MCF-7	breast:
2	chr22:31890586..31892478-chr6:26238591..26241305,2	MCF-7	breast:
3	chr22:31849740..31852347-chr22:31891078..31892965,2	K562	blood:
4	chr22:31890350..31892385-chr22:32144551..32147460,2	K562	blood:

Variant related genes	Relation type
SFI1	TF binding region
ENSG00000240591	Chromatin interaction
ENSG00000198327	Chromatin interaction
ENSG00000183530	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000184708	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1018490	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs13057504	0.87[AMR][1000 genomes]
rs1543416	0.82[JPT][hapmap]
rs16989527	0.88[YRI][hapmap]
rs16989611	1.00[YRI][hapmap]
rs16989642	1.00[YRI][hapmap]
rs16989647	1.00[YRI][hapmap]
rs16989655	1.00[YRI][hapmap]
rs16989698	0.85[LWK][hapmap];0.88[YRI][hapmap]
rs1968023	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs2273249	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2273251	0.80[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs2899164	0.80[CEU][hapmap];0.91[CHB][hapmap]
rs34538851	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34545960	0.80[AMR][1000 genomes]
rs4602315	0.85[LWK][hapmap]
rs4603880	0.83[GIH][hapmap];0.91[TSI][hapmap]
rs4820983	0.82[JPT][hapmap]
rs5749267	0.83[AMR][1000 genomes]
rs5749268	0.83[AMR][1000 genomes]
rs5749270	0.83[AMR][1000 genomes]
rs5749283	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749291	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749298	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753601	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5753609	0.85[TSI][hapmap]
rs5753610	0.83[AMR][1000 genomes]
rs5753612	0.80[AMR][1000 genomes]
rs5753613	0.83[AMR][1000 genomes]
rs5753615	0.87[AMR][1000 genomes]
rs5753618	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs5753621	0.88[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753628	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753631	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753632	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs5753639	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs5753648	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5753661	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753664	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753665	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753666	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753686	0.82[JPT][hapmap]
rs5753698	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs5753723	0.83[CEU][hapmap]
rs5994394	0.83[AMR][1000 genomes]
rs5998058	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs5998067	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs714909	0.85[GIH][hapmap];0.91[TSI][hapmap]
rs7284622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7285619	0.80[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes]
rs7293171	0.80[AMR][1000 genomes]
rs737887	0.85[GIH][hapmap];0.87[TSI][hapmap]
rs738657	0.80[CEU][hapmap]
rs8138525	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs8139625	0.87[AMR][1000 genomes]
rs8142121	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9606839	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs9606843	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9606846	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9606847	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9606848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9606852	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9609286	0.87[AMR][1000 genomes]
rs9609295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609299	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609301	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609303	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9609329	1.00[CEU][hapmap];0.95[JPT][hapmap]

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	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3334530	chr22:31889221-31909085	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9609296	PISD	cis	cerebellum	SCAN
rs9609296	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs9609296	SFI1	cis	cerebellum	SCAN
rs9609296	SFI1	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31887000-31892000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr22:31887000-31892000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:31887000-31892000	Weak transcription	Lung	lung
4	chr22:31887000-31892000	Weak transcription	Pancreas	Pancrea
5	chr22:31887200-31892000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr22:31887400-31891800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr22:31887400-31892000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr22:31887400-31892000	Weak transcription	Spleen	Spleen
9	chr22:31889600-31891800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr22:31889600-31891800	Enhancers	Fetal Thymus	thymus
11	chr22:31890200-31891800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:31890200-31891800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr22:31890400-31891800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr22:31890800-31891800	Weak transcription	Psoas Muscle	Psoas
15	chr22:31891200-31891800	Enhancers	Primary hematopoietic stem cells	blood
16	chr22:31891200-31891800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr22:31891200-31891800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr22:31891200-31893200	Active TSS	K562	blood
19	chr22:31891400-31891800	Enhancers	Liver	Liver
20	chr22:31891400-31891800	Enhancers	Colonic Mucosa	Colon
21	chr22:31891400-31891800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr22:31891400-31891800	Enhancers	Fetal Muscle Leg	muscle
23	chr22:31891400-31891800	Enhancers	Left Ventricle	heart
24	chr22:31891400-31891800	Enhancers	Right Atrium	heart
25	chr22:31891400-31891800	Flanking Active TSS	Dnd41	blood
26	chr22:31891400-31891800	Flanking Active TSS	GM12878-XiMat	blood
27	chr22:31891400-31892000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr22:31891400-31892200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr22:31891400-31892200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr22:31891400-31892200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr22:31891400-31892400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr22:31891400-31892400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr22:31891400-31893000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr22:31891400-31893000	Active TSS	Brain Angular Gyrus	brain
35	chr22:31891400-31893000	Active TSS	Brain Anterior Caudate	brain
36	chr22:31891400-31893000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr22:31891400-31893200	Active TSS	NHEK	skin
38	chr22:31891400-31893400	Active TSS	Hela-S3	cervix
39	chr22:31891600-31891800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr22:31891600-31891800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr22:31891600-31891800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr22:31891600-31891800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr22:31891600-31891800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr22:31891600-31891800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr22:31891600-31891800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr22:31891600-31891800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr22:31891600-31891800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr22:31891600-31891800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr22:31891600-31891800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr22:31891600-31891800	Flanking Active TSS	Brain Cingulate Gyrus	brain

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