Variant report

Variant	rs4978536
Chromosome Location	chr9:115982403-115982404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

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	POU2F2	chr9:115982184-115982630	GM12878	blood:	n/a	n/a
3	EBF1	chr9:115981369-115982712	GM12878	blood:	n/a	n/a
4	ATF2	chr9:115981374-115982764	GM12878	blood:	n/a	n/a
5	MXI1	chr9:115981145-115984347	GM12878	blood:	n/a	n/a
6	PML	chr9:115981826-115984110	GM12878	blood:	n/a	chr9:115983963-115983971
7	SPI1	chr9:115982153-115982524	GM12891	blood:	n/a	n/a
8	MAFK	chr9:115982353-115982535	K562	blood:	n/a	n/a
9	MEF2A	chr9:115982093-115982623	GM12878	blood:	n/a	n/a
10	FOS	chr9:115982222-115982512	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr9:115982237-115982549	MCF10A-Er-Src	breast:	n/a	n/a
12	EP300	chr9:115981398-115982763	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
13	POLR2A	chr9:115981373-115984128	GM12891	blood:	n/a	n/a
14	RCOR1	chr9:115981341-115982668	GM12878	blood:	n/a	n/a
15	RELA	chr9:115982122-115984391	GM18951	blood:	n/a	n/a
16	MAX	chr9:115982245-115982616	K562	blood:	n/a	n/a
17	MTA3	chr9:115982162-115983011	GM12878	blood:	n/a	n/a
18	RUNX3	chr9:115981378-115983926	GM12878	blood:	n/a	n/a
19	POLR2A	chr9:115982266-115982881	GM12878	blood:	n/a	n/a
20	NFATC1	chr9:115981569-115982664	GM12878	blood:	n/a	n/a
21	POLR2A	chr9:115982203-115984095	GM18505	blood:	n/a	n/a
22	BATF	chr9:115982206-115982623	GM12878	blood:	n/a	n/a
23	MXI1	chr9:115981681-115985060	SK-N-SH	brain:	n/a	n/a
24	POU2F2	chr9:115982273-115982616	GM12878	blood:	n/a	n/a
25	STAT1	chr9:115982379-115982915	GM12878	blood:	n/a	chr9:115982620-115982627
26	MYC	chr9:115981797-115982601	K562	blood:	n/a	n/a
27	EP300	chr9:115982158-115983016	GM12878	blood:	n/a	n/a
28	MYC	chr9:115982284-115982623	NB4	blood:	n/a	n/a
29	POU2F2	chr9:115982251-115982500	GM12878	blood:	n/a	n/a
30	MAX	chr9:115981479-115984076	GM12878	blood:	n/a	chr9:115983813-115983823
31	MAX	chr9:115981823-115982464	K562	blood:	n/a	n/a
32	CEBPB	chr9:115982248-115982576	IMR90	lung:	n/a	n/a
33	MAX	chr9:115982303-115982441	K562	blood:	n/a	n/a
34	POLR2A	chr9:115982355-115985172	IMR90	lung:	n/a	n/a
35	EP300	chr9:115981321-115983093	GM12878	blood:	n/a	chr9:115981630-115981639 chr9:115981629-115981643
36	BATF	chr9:115982119-115982632	GM12878	blood:	n/a	n/a
37	NFIC	chr9:115981379-115982852	GM12878	blood:	n/a	n/a
38	RELA	chr9:115982255-115983851	GM19193	blood:	n/a	n/a
39	CHD1	chr9:115981494-115983650	GM12878	blood:	n/a	n/a
40	BHLHE40	chr9:115982127-115984239	GM12878	blood:	n/a	chr9:115984103-115984119
41	FOXM1	chr9:115981374-115982779	GM12878	blood:	n/a	n/a
42	MTA3	chr9:115981314-115984189	GM12878	blood:	n/a	n/a
43	IRF1	chr9:115982050-115982518	K562	blood:	n/a	n/a
44	MAX	chr9:115982324-115982487	Hela-S3	cervix:	n/a	n/a
45	STAT3	chr9:115981472-115982969	GM12878	blood:	n/a	chr9:115982276-115982284 chr9:115982620-115982627
46	POLR2A	chr9:115981548-115984508	GM12878	blood:	n/a	n/a
47	MYC	chr9:115982294-115983044	MCF10A-Er-Src	breast:	n/a	n/a
48	SPI1	chr9:115982243-115982455	GM12878	blood:	n/a	n/a
49	SP1	chr9:115982127-115982658	GM12878	blood:	n/a	n/a
50	ZNF143	chr9:115982232-115982618	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

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	chr9:115968725..115971196-chr9:115981878..115984279,2	MCF-7	breast:
4	chr9:115981081..115983502-chr9:115983537..115987172,3	MCF-7	breast:
5	chr9:115981852..115985156-chr9:116171660..116173942,3	MCF-7	breast:
6	chr9:115982263..115984734-chr9:116036359..116038354,4	MCF-7	breast:
7	chr9:115978706..115980364-chr9:115981064..115982891,2	K562	blood:
8	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
9	chr9:115974346..115976683-chr9:115980205..115982463,2	MCF-7	breast:
10	chr9:115949400..115951556-chr9:115979789..115982738,2	MCF-7	breast:

No data

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

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10081797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[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]
rs10116039	0.82[GIH][hapmap]
rs10121845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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];0.92[JPT][hapmap];0.89[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];0.92[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	0.88[ASW][hapmap];0.87[GIH][hapmap];0.90[YRI][hapmap]
rs10817470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][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];0.92[JPT][hapmap];0.89[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]
rs3810914	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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][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];0.92[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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	0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4978536	SVEP1	cis	parietal	SCAN
rs4978536	ZNF618	cis	cerebellum	SCAN
rs4978536	CDC26	cis	parietal	SCAN
rs4978536	CDC26	cis	cerebellum	SCAN
rs4978536	PRPF4	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115945600-115982800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:115950800-115982800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:115951000-115982800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:115970000-115982800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:115972600-115982800	Weak transcription	Gastric	stomach
6	chr9:115973200-115982600	Weak transcription	Ovary	ovary
7	chr9:115973800-115982800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:115973800-115982800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:115973800-115982800	Weak transcription	Lung	lung
10	chr9:115980200-115982800	Enhancers	Primary B cells from peripheral blood	blood
11	chr9:115980800-115982600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr9:115980800-115982800	Enhancers	Stomach Mucosa	stomach
13	chr9:115981200-115983200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr9:115981200-115983400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr9:115981200-115985600	Active TSS	GM12878-XiMat	blood
16	chr9:115981400-115982600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr9:115981400-115982800	Flanking Active TSS	Dnd41	blood
18	chr9:115981400-115983000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:115981400-115983200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr9:115981400-115983400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:115981600-115983000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:115981800-115982600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr9:115981800-115982600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr9:115981800-115982600	Flanking Active TSS	HepG2	liver
25	chr9:115981800-115982800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:115981800-115982800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr9:115981800-115983000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr9:115981800-115983000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:115981800-115983000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr9:115981800-115983000	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr9:115981800-115983000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr9:115981800-115983200	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr9:115981800-115983200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr9:115981800-115983200	Flanking Active TSS	Osteobl	bone
35	chr9:115981800-115983400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr9:115981800-115983400	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr9:115981800-115983400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:115982000-115982600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:115982000-115982600	Enhancers	Primary T cells fromperipheralblood	blood
40	chr9:115982000-115982600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:115982000-115982600	Enhancers	Fetal Stomach	stomach
42	chr9:115982000-115982600	Active TSS	Right Atrium	heart
43	chr9:115982000-115982600	Flanking Active TSS	Thymus	Thymus
44	chr9:115982000-115982800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:115982000-115982800	Enhancers	Small Intestine	intestine
46	chr9:115982000-115982800	Flanking Active TSS	HMEC	breast
47	chr9:115982000-115983000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:115982000-115983000	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr9:115982000-115983000	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr9:115982000-115983000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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