Variant report

Variant	rs4077176
Chromosome Location	chr9:95827196-95827197
allele	C/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	POLR2A	chr9:95826580-95827196	GM12891	blood:	n/a	n/a
2	POLR2A	chr9:95826489-95827220	GM12878	blood:	n/a	n/a
3	RCOR1	chr9:95826619-95827205	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:95826506-95827217	GM18951	blood:	n/a	n/a
5	ELF1	chr9:95826470-95827454	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:95825693-95827281	GM12878	blood:	n/a	n/a
7	POU2F2	chr9:95826546-95827303	GM12891	blood:	n/a	n/a
8	ESRRA	chr9:95825379-95827466	GM12878	blood:	n/a	chr9:95826281-95826295 chr9:95826280-95826296 chr9:95826863-95826879 chr9:95826863-95826879 chr9:95826279-95826297 chr9:95825948-95825958 chr9:95826735-95826751 chr9:95826281-95826300
9	PAX5	chr9:95826477-95827256	GM12878	blood:	n/a	chr9:95827002-95827011
10	PML	chr9:95826453-95827494	GM12878	blood:	n/a	chr9:95827238-95827246
11	POLR2A	chr9:95826606-95827259	HL-60	blood:	n/a	n/a
12	BHLHE40	chr9:95826663-95827290	K562	blood:	n/a	chr9:95826966-95826982
13	NR2C2	chr9:95826640-95827206	GM12878	blood:	n/a	n/a
14	POLR2A	chr9:95826619-95827459	GM12878	blood:	n/a	n/a
15	POLR2A	chr9:95826540-95827497	GM18505	blood:	n/a	n/a
16	CHD2	chr9:95826565-95827491	GM12878	blood:	n/a	n/a
17	MTA3	chr9:95826465-95827331	GM12878	blood:	n/a	n/a
18	ATF2	chr9:95826537-95827216	GM12878	blood:	n/a	n/a
19	RCOR1	chr9:95826558-95827197	K562	blood:	n/a	n/a
20	POLR2A	chr9:95826549-95827264	GM12878	blood:	n/a	n/a
21	POLR2A	chr9:95826487-95827262	GM12892	blood:	n/a	n/a
22	POLR2A	chr9:95826610-95827294	GM15510	blood:	n/a	n/a
23	POLR2A	chr9:95826515-95827282	GM12891	blood:	n/a	n/a
24	MAX	chr9:95826588-95827259	NB4	blood:	n/a	chr9:95826643-95826652
25	TEAD4	chr9:95826519-95827204	K562	blood:	n/a	n/a
26	RUNX3	chr9:95826569-95827262	GM12878	blood:	n/a	n/a
27	FOXM1	chr9:95826501-95827213	GM12878	blood:	n/a	n/a
28	SPI1	chr9:95826595-95827343	HL-60	blood:	n/a	chr9:95827002-95827009
29	CUX1	chr9:95826717-95827306	K562	blood:	n/a	n/a
30	BHLHE40	chr9:95826630-95827206	GM12878	blood:	n/a	chr9:95826966-95826982
31	STAT5A	chr9:95826559-95827306	GM12878	blood:	n/a	chr9:95827004-95827011
32	WRNIP1	chr9:95826486-95827214	GM12878	blood:	n/a	n/a
33	POLR2A	chr9:95826405-95827312	GM12892	blood:	n/a	n/a
34	ELF1	chr9:95826588-95827224	GM12878	blood:	n/a	n/a
35	RUNX3	chr9:95826525-95827364	GM12878	blood:	n/a	n/a
36	POLR2A	chr9:95826572-95827349	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95826956..95829616-chr9:95830971..95832502,2	K562	blood:
2	chr9:95824581..95826118-chr9:95826533..95829514,2	MCF-7	breast:
3	chr9:95825270..95827646-chr9:95832621..95835628,3	K562	blood:

Variant related genes	Relation type
SUSD3	TF binding region
ENSG00000157303	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10992622	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992623	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1131773	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12375973	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs12378451	0.90[JPT][hapmap]
rs12555029	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1970623	0.86[JPT][hapmap]
rs4077177	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077637	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4077811	0.92[CHD][hapmap];0.85[JPT][hapmap]
rs4078501	0.86[GIH][hapmap]
rs4341217	0.89[CHD][hapmap];0.91[JPT][hapmap]
rs4636265	0.85[CHD][hapmap];0.93[JPT][hapmap]
rs4743886	0.86[JPT][hapmap]
rs56000948	0.88[ASN][1000 genomes]
rs57327517	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60671060	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019574	0.85[ASN][1000 genomes]
rs7025686	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7036869	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7046192	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs7046328	0.85[CHB][hapmap]
rs7859109	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs7870697	0.88[ASN][1000 genomes]
rs9696357	0.86[CHD][hapmap];1.00[JPT][hapmap]

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
rs4077176	SUSD3	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95820800-95827600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr9:95821000-95827400	Flanking Active TSS	GM12878-XiMat	blood
3	chr9:95821600-95827400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr9:95821600-95827600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr9:95821800-95827400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr9:95822000-95834200	Weak transcription	Esophagus	oesophagus
7	chr9:95822000-95834200	Weak transcription	Right Atrium	heart
8	chr9:95822400-95828600	Enhancers	Primary hematopoietic stem cells	blood
9	chr9:95822600-95834400	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:95822800-95831000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:95823400-95827800	Weak transcription	Right Ventricle	heart
12	chr9:95824000-95833800	Weak transcription	Ovary	ovary
13	chr9:95824200-95827200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:95824400-95827200	Weak transcription	Lung	lung
15	chr9:95824600-95854000	Weak transcription	Gastric	stomach
16	chr9:95824800-95833200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:95825200-95829000	Weak transcription	Pancreas	Pancrea
18	chr9:95825200-95834000	Weak transcription	Liver	Liver
19	chr9:95825400-95827600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr9:95825400-95828200	Enhancers	Duodenum Mucosa	Duodenum
21	chr9:95825600-95827400	Enhancers	K562	blood
22	chr9:95825600-95827800	Enhancers	Spleen	Spleen
23	chr9:95825800-95828600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr9:95826000-95827400	Flanking Active TSS	Dnd41	blood
25	chr9:95826000-95827800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr9:95826200-95827200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr9:95826200-95827200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:95826200-95827400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:95826200-95828000	Weak transcription	Brain Substantia Nigra	brain
30	chr9:95826200-95828400	Strong transcription	Fetal Intestine Small	intestine
31	chr9:95826400-95828400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr9:95826600-95827200	Enhancers	HSMM	muscle
33	chr9:95826600-95827400	Flanking Active TSS	Fetal Thymus	thymus
34	chr9:95826600-95828000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr9:95826600-95828200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:95826600-95828200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr9:95826600-95828400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:95826800-95828000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:95826800-95828200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:95826800-95828200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr9:95826800-95828400	Enhancers	Adipose Nuclei	Adipose
42	chr9:95827000-95827200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:95827000-95827200	Enhancers	Primary B cells from cord blood	blood
44	chr9:95827000-95827200	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr9:95827000-95827200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:95827000-95827200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr9:95827000-95827400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:95827000-95827400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:95827000-95827400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr9:95827000-95827400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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