Variant report

Variant	rs12375973
Chromosome Location	chr9:95854013-95854014
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	CBX3	chr9:95853481-95854384	HCT-116	colon:	n/a	n/a
2	STAT3	chr9:95853808-95854031	MCF10A-Er-Src	breast:	n/a	chr9:95853900-95853911
3	RUNX3	chr9:95853678-95854326	GM12878	blood:	n/a	n/a
4	FOS	chr9:95853730-95854124	MCF10A-Er-Src	breast:	n/a	chr9:95853925-95853936 chr9:95853907-95853918
5	FOSL2	chr9:95853534-95854457	A549	lung:	n/a	chr9:95854250-95854258 chr9:95853926-95853937
6	JUN	chr9:95853749-95854255	K562	blood:	n/a	n/a
7	ATF2	chr9:95853650-95854118	GM12878	blood:	n/a	n/a
8	NFIC	chr9:95853585-95854162	GM12878	blood:	n/a	n/a
9	JUND	chr9:95853780-95854304	HepG2	liver:	n/a	chr9:95853925-95853936 chr9:95854250-95854258 chr9:95853907-95853918
10	MAZ	chr9:95853864-95854159	HepG2	liver:	n/a	n/a
11	RFX5	chr9:95853946-95854083	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:95853762-95854379	GM12878	blood:	n/a	n/a
13	MYC	chr9:95853808-95854033	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr9:95853753-95854116	HCT-116	colon:	n/a	n/a
15	USF1	chr9:95853704-95854105	A549	lung:	n/a	n/a
16	RCOR1	chr9:95853761-95854241	Hela-S3	cervix:	n/a	n/a
17	JUND	chr9:95853574-95854471	SK-N-SH	brain:	n/a	chr9:95853925-95853936 chr9:95854250-95854258 chr9:95853907-95853918
18	JUND	chr9:95853571-95854295	SK-N-SH	brain:	n/a	chr9:95853925-95853936 chr9:95854250-95854258 chr9:95853907-95853918
19	JUN	chr9:95853683-95854153	Hela-S3	cervix:	n/a	n/a
20	JUN	chr9:95853795-95854052	HepG2	liver:	n/a	n/a
21	POLR2A	chr9:95853758-95854075	U87	brain:	n/a	n/a
22	JUND	chr9:95853696-95854215	A549	lung:	n/a	chr9:95853925-95853936 chr9:95853907-95853918
23	TCF12	chr9:95853752-95854027	GM12878	blood:	n/a	n/a
24	NFATC1	chr9:95853685-95854149	GM12878	blood:	n/a	n/a
25	POLR2A	chr9:95853860-95854030	MCF10A-Er-Src	breast:	n/a	n/a
26	FOSL2	chr9:95853596-95854452	SK-N-SH	brain:	n/a	chr9:95854250-95854258 chr9:95853926-95853937
27	FOSL2	chr9:95853720-95854120	A549	lung:	n/a	chr9:95853926-95853937
28	POLR2A	chr9:95853662-95854024	U87	brain:	n/a	n/a
29	PAX5	chr9:95853611-95854339	GM12878	blood:	n/a	n/a
30	NFIC	chr9:95853658-95854229	SK-N-SH	brain:	n/a	n/a
31	SPI1	chr9:95853803-95854068	GM12878	blood:	n/a	n/a
32	YY1	chr9:95853733-95854077	GM12892	blood:	n/a	n/a
33	FOSL2	chr9:95853631-95854523	MCF-7	breast:	n/a	chr9:95854250-95854258 chr9:95853926-95853937
34	BATF	chr9:95853705-95854127	GM12878	blood:	n/a	n/a
35	JUND	chr9:95853542-95854530	HCT-116	colon:	n/a	chr9:95853925-95853936 chr9:95854250-95854258 chr9:95853907-95853918
36	ATF2	chr9:95853596-95854166	GM12878	blood:	n/a	n/a
37	EP300	chr9:95853795-95854062	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:95853692-95854069	SK-N-SH	brain:	n/a	n/a
39	JUND	chr9:95853693-95854232	Hela-S3	cervix:	n/a	chr9:95853925-95853936 chr9:95853907-95853918
40	BCL11A	chr9:95853701-95854075	GM12878	blood:	n/a	n/a
41	USF1	chr9:95853632-95854357	HCT-116	colon:	n/a	n/a
42	FOSL2	chr9:95853669-95854155	HepG2	liver:	n/a	chr9:95853926-95853937
43	POLR2A	chr9:95853700-95854075	U87	brain:	n/a	n/a
44	JUND	chr9:95853764-95854144	A549	lung:	n/a	chr9:95853925-95853936 chr9:95853907-95853918
45	MYC	chr9:95853804-95854044	MCF10A-Er-Src	breast:	n/a	n/a
46	BHLHE40	chr9:95853828-95854053	GM12878	blood:	n/a	n/a
47	JUN	chr9:95853704-95854112	K562	blood:	n/a	n/a
48	RXRA	chr9:95853710-95854319	SK-N-SH	brain:	n/a	n/a
49	SPI1	chr9:95853882-95854048	GM12878	blood:	n/a	n/a
50	FOSL2	chr9:95853663-95854229	SK-N-SH	brain:	n/a	chr9:95853926-95853937

No.	Distal block	Cell Line	Cell type
1	chr9:95853194..95855867-chr9:95863177..95866078,2	MCF-7	breast:
2	chr9:95828110..95830344-chr9:95853577..95856125,2	K562	blood:
3	chr9:95816364..95826268-chr9:95852309..95863275,20	MCF-7	breast:
4	chr9:95838033..95840952-chr9:95852515..95855159,2	MCF-7	breast:
5	chr9:95852876..95854793-chr9:95906541..95909391,2	K562	blood:

Variant related genes	Relation type
C9orf89	TF binding region
ENSG00000157303	Chromatin interaction
ENSG00000203364	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10821066	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992622	0.86[CHD][hapmap]
rs10992623	0.86[CHD][hapmap]
rs10992626	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992628	0.98[ASN][1000 genomes]
rs1131773	0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12004054	0.90[ASN][1000 genomes]
rs12352182	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12378451	0.90[JPT][hapmap]
rs16908779	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1970623	0.86[JPT][hapmap]
rs28468656	0.95[ASN][1000 genomes]
rs4077176	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4077177	0.81[CEU][hapmap];0.82[CHD][hapmap]
rs4077811	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4078501	0.82[ASN][1000 genomes]
rs4341217	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4636265	0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4743886	0.86[JPT][hapmap]
rs57866297	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61478314	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479448	0.81[EUR][1000 genomes]
rs6479450	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7025686	0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7036869	0.86[CHD][hapmap]
rs7046192	0.85[CHD][hapmap];0.82[EUR][1000 genomes]
rs7849306	0.97[ASN][1000 genomes]
rs7859109	0.89[CHD][hapmap]
rs7870953	0.82[EUR][1000 genomes]
rs9695137	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9696341	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9696357	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12375973	SUSD3	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95834400-95857400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95836200-95855600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:95840400-95857000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:95845200-95857200	Weak transcription	Small Intestine	intestine
5	chr9:95845800-95854400	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:95845800-95854800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:95846200-95855000	Weak transcription	Fetal Lung	lung
8	chr9:95846400-95857000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:95848400-95854600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:95848400-95854800	Weak transcription	Fetal Intestine Large	intestine
11	chr9:95848400-95855000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr9:95848400-95855000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr9:95848400-95855400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr9:95848400-95855800	Weak transcription	Liver	Liver
15	chr9:95848600-95855000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:95848600-95857000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:95848800-95855400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:95848800-95855600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:95849400-95854400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:95849400-95855200	Weak transcription	Fetal Kidney	kidney
21	chr9:95849400-95857400	Weak transcription	Ovary	ovary
22	chr9:95849600-95855000	Weak transcription	Colonic Mucosa	Colon
23	chr9:95849600-95855200	Weak transcription	Fetal Intestine Small	intestine
24	chr9:95849800-95854400	Weak transcription	Fetal Thymus	thymus
25	chr9:95850400-95855400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:95851000-95854400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:95851000-95855000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:95851400-95855200	Weak transcription	Thymus	Thymus
29	chr9:95851600-95854800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:95851800-95855400	Weak transcription	K562	blood
31	chr9:95852000-95855000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:95852200-95855400	Weak transcription	Primary T cells from cord blood	blood
33	chr9:95852400-95854400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:95852600-95856800	Enhancers	Primary B cells from peripheral blood	blood
35	chr9:95853200-95854400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
36	chr9:95853200-95854800	ZNF genes & repeats	GM12878-XiMat	blood
37	chr9:95853400-95854200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:95853400-95854200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:95853400-95854400	ZNF genes & repeats	Placenta	Placenta
40	chr9:95853400-95854800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:95853400-95857000	Enhancers	Primary B cells from cord blood	blood
42	chr9:95853400-95857200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr9:95853400-95857200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr9:95853600-95855200	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr9:95853600-95856800	Enhancers	HepG2	liver
46	chr9:95853600-95857200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr9:95853800-95854200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:95853800-95854200	Enhancers	A549	lung
49	chr9:95853800-95855000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:95853800-95857200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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