Variant report

Variant	rs296891
Chromosome Location	chr9:86597208-86597209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr9:86597097-86597520	K562	blood:	n/a	chr9:86597103-86597114
2	MAFK	chr9:86597051-86597367	HepG2	liver:	n/a	chr9:86597224-86597238 chr9:86597225-86597236 chr9:86597225-86597236
3	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
4	RCOR1	chr9:86594122-86597693	K562	blood:	n/a	n/a
5	ZNF384	chr9:86597151-86597658	K562	blood:	n/a	n/a
6	POLR2A	chr9:86597125-86597601	K562	blood:	n/a	n/a
7	MAFK	chr9:86596397-86597394	K562	blood:	n/a	chr9:86596666-86596676 chr9:86597224-86597238 chr9:86596666-86596675 chr9:86597225-86597236 chr9:86597225-86597236
8	JUND	chr9:86594377-86597401	K562	blood:	n/a	chr9:86596666-86596678 chr9:86594436-86594445 chr9:86595324-86595338 chr9:86597230-86597239 chr9:86595271-86595280
9	POLR2A	chr9:86597018-86597348	K562	blood:	n/a	n/a
10	SETDB1	chr9:86596977-86597420	U2OS	brain:	n/a	n/a
11	MAFK	chr9:86596449-86597346	IMR90	lung:	n/a	chr9:86596666-86596676 chr9:86597224-86597238 chr9:86596666-86596675 chr9:86597225-86597236 chr9:86597225-86597236
12	TBP	chr9:86597037-86597481	K562	blood:	n/a	n/a
13	CEBPB	chr9:86597139-86597518	K562	blood:	n/a	n/a
14	MAFF	chr9:86596338-86597365	K562	blood:	n/a	n/a
15	TEAD4	chr9:86597020-86597424	K562	blood:	n/a	n/a
16	UBTF	chr9:86597117-86597471	K562	blood:	n/a	n/a
17	MAFF	chr9:86597068-86597358	HepG2	liver:	n/a	n/a
18	RPC155	chr9:86597098-86597799	K562	blood:	n/a	n/a
19	ATF1	chr9:86597081-86597370	K562	blood:	n/a	n/a
20	EP300	chr9:86596144-86597409	K562	blood:	n/a	n/a
21	HCFC1	chr9:86597033-86597358	K562	blood:	n/a	n/a
22	POLR2A	chr9:86597028-86597618	K562	blood:	n/a	n/a
23	ELF1	chr9:86597162-86597623	K562	blood:	n/a	n/a
24	MAFK	chr9:86597055-86597315	HepG2	liver:	n/a	chr9:86597224-86597238 chr9:86597225-86597236 chr9:86597225-86597236
25	POLR2A	chr9:86593163-86597264	GM12891	blood:	n/a	n/a
26	EP300	chr9:86596260-86597430	GM12878	blood:	n/a	n/a
27	TBL1XR1	chr9:86596193-86597244	K562	blood:	n/a	n/a
28	CUX1	chr9:86596581-86597284	K562	blood:	n/a	n/a
29	MYC	chr9:86594151-86597779	K562	blood:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
30	MAFK	chr9:86594217-86597217	Hela-S3	cervix:	n/a	chr9:86596666-86596676 chr9:86596666-86596675
31	MAZ	chr9:86596610-86597421	K562	blood:	n/a	n/a
32	ARID3A	chr9:86597040-86597385	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:86597173-86597223	AG04449	skin:	fetal
2	chr9:86597173-86597223	AG09309	skin:	n/a
3	chr9:86597173-86597223	CMK	blood:	n/a
4	chr9:86597173-86597223	LNCaP	prostate:	n/a
5	chr9:86597173-86597223	ECC-1	luminal epithelium:	n/a
6	chr9:86597173-86597223	HNPCEpiC	eye:	n/a
7	chr9:86597173-86597223	NHBE	bronchial:	n/a
8	chr9:86597173-86597223	GM19239	blood:	n/a
9	chr9:86597173-86597223	BJ	skin:	n/a
10	chr9:86597173-86597223	HRPEpiC	eye:	n/a
11	chr9:86597173-86597223	U87	brain:	n/a
12	chr9:86597173-86597223	HUVEC	blood vessel:	n/a
13	chr9:86597173-86597223	GM12892	blood:	n/a
14	chr9:86597173-86597223	Hepatocyte	liver:	n/a
15	chr9:86597173-86597223	MCF-7	breast:	n/a
16	chr9:86597173-86597223	NB4	blood:	n/a
17	chr9:86597173-86597223	AG09319	gingival:	n/a
18	chr9:86597173-86597223	GM12878	blood:	n/a
19	chr9:86597173-86597223	IMR90	lung:	fetal
20	chr9:86597173-86597223	BE2_C	brain:	n/a
21	chr9:86597173-86597223	Caco-2	colon:	n/a
22	chr9:86597173-86597223	AoSMC	blood vessel:	n/a
23	chr9:86597173-86597223	GM12891	blood:	n/a
24	chr9:86597173-86597223	AG10803	skin:	n/a
25	chr9:86597173-86597223	AG04450	lung:	fetal
26	chr9:86597173-86597223	PFSK-1	brain:	n/a
27	chr9:86597173-86597223	RPTEC	kidney:	n/a
28	chr9:86597173-86597223	HRE	kidney:	n/a
29	chr9:86597173-86597223	HEK293	kidney:	embryo
30	chr9:86597173-86597223	NH-A	brain:	n/a
31	chr9:86597173-86597223	NT2-D1	testis:	n/a
32	chr9:86597173-86597223	Jurkat	blood:	n/a
33	chr9:86597173-86597223	HMEC	breast:	n/a
34	chr9:86597173-86597223	K562	blood:	n/a
35	chr9:86597173-86597223	HAEpiC	amniotic membrane:	n/a
36	chr9:86597173-86597223	ProgFib	skin:	n/a
37	chr9:86597173-86597223	SK-N-MC	brain:	n/a
38	chr9:86597173-86597223	PrEC	prostate:	n/a
39	chr9:86597173-86597223	T-47D	breast:	n/a
40	chr9:86597173-86597223	HepG2	liver:	n/a
41	chr9:86597173-86597223	ovcar-3	ovarian:	n/a
42	chr9:86597173-86597223	NHDF-neo	bronchial:	n/a
43	chr9:86597173-86597223	HCF	heart:	n/a
44	chr9:86597173-86597223	SK-N-SH	brain:	n/a
45	chr9:86597173-86597223	HCPEpiC	choroid plexus:	n/a
46	chr9:86597173-86597223	PANC-1	pancreas:	n/a
47	chr9:86597173-86597223	HRCEpiC	kidney:	n/a
48	chr9:86597173-86597223	A549	lung:	n/a
49	chr9:86597173-86597223	SKMC	muscle:	n/a
50	chr9:86597173-86597223	HL-60	blood:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
2	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
3	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
4	chr9:86596431..86597964-chr9:86790384..86792267,2	MCF-7	breast:
5	chr9:86592736..86597542-chr9:86606160..86610925,6	K562	blood:
6	chr9:86533247..86537973-chr9:86593370..86597981,20	MCF-7	breast:

No data

Variant related genes	Relation type
HNRNPK	TF binding region
HNRNPK	CpG island
ENSG00000165115	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000202523	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10124390	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10125673	0.88[ASN][1000 genomes]
rs10780639	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10780640	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868077	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]
rs10868079	0.87[CHB][hapmap]
rs11792634	0.81[CHB][hapmap]
rs12004439	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12551039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1572030	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1572031	0.87[CHB][hapmap]
rs177042	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065516	0.87[CHB][hapmap]
rs2780142	0.87[CHB][hapmap]
rs295274	0.87[CHB][hapmap]
rs295291	0.83[CHB][hapmap]
rs296885	0.87[CHB][hapmap]
rs296892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3180887	0.82[LWK][hapmap]
rs4297107	0.83[CHB][hapmap]
rs4877814	0.95[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877815	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5018100	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6559750	0.87[CHB][hapmap]
rs6559753	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6559754	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6559756	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7020841	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7021189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026436	0.83[CHB][hapmap]
rs7045008	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754144	0.87[CHB][hapmap]
rs7864367	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7869387	0.87[CHB][hapmap]
rs7875011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875289	0.87[CHB][hapmap]
rs796000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796002	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314723	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs296891	C9orf64	cis	cerebellum	SCAN
rs296891	C9orf64	cis	parietal	SCAN
rs296891	RMI1	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86592400-86597600	Active TSS	Fetal Brain Female	brain
2	chr9:86593000-86597400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr9:86593000-86598600	Active TSS	GM12878-XiMat	blood
4	chr9:86594200-86598400	Active TSS	K562	blood
5	chr9:86594400-86597400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
7	chr9:86596600-86597400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr9:86596600-86597400	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr9:86596600-86597400	Enhancers	Stomach Mucosa	stomach
10	chr9:86596600-86601800	Weak transcription	Pancreas	Pancrea
11	chr9:86596600-86603200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:86596600-86610600	Weak transcription	Esophagus	oesophagus
13	chr9:86596600-86613400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:86596600-86613800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:86596600-86616000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:86596600-86617000	Weak transcription	Lung	lung
17	chr9:86596600-86618200	Weak transcription	Ovary	ovary
18	chr9:86596600-86619600	Weak transcription	Gastric	stomach
19	chr9:86596800-86597400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:86596800-86597400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:86596800-86597600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr9:86596800-86597800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr9:86596800-86598000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr9:86596800-86598000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:86596800-86601200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr9:86596800-86601200	Weak transcription	Liver	Liver
27	chr9:86596800-86601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:86596800-86601800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr9:86596800-86601800	Weak transcription	Left Ventricle	heart
30	chr9:86596800-86601800	Weak transcription	HSMM	muscle
31	chr9:86596800-86602000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr9:86596800-86603200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:86596800-86603200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:86596800-86603200	Weak transcription	Fetal Thymus	thymus
35	chr9:86596800-86605400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:86596800-86606600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:86596800-86613200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:86596800-86614400	Weak transcription	HSMMtube	muscle
39	chr9:86596800-86616000	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:86596800-86616200	Weak transcription	Brain Angular Gyrus	brain
41	chr9:86596800-86616200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:86596800-86619600	Weak transcription	Small Intestine	intestine
43	chr9:86596800-86621400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:86597000-86597400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:86597000-86597400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr9:86597000-86597400	Enhancers	Primary B cells from cord blood	blood
48	chr9:86597000-86597400	Enhancers	Psoas Muscle	Psoas
49	chr9:86597000-86597400	Flanking Active TSS	HepG2	liver
50	chr9:86597000-86597600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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