Variant report

Variant	rs357522
Chromosome Location	chr9:98189458-98189459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:191)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:191 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:98188828-98189528	GM12892	blood:	n/a	n/a
2	MAX	chr9:98188548-98189755	HCT-116	colon:	n/a	n/a
3	CBX3	chr9:98188729-98189770	HCT-116	colon:	n/a	n/a
4	POLR2A	chr9:98188723-98189738	K562	blood:	n/a	n/a
5	EP300	chr9:98188864-98189620	ECC-1	luminal epithelium:	n/a	n/a
6	CHD2	chr9:98188481-98189501	Hela-S3	cervix:	n/a	n/a
7	HEY1	chr9:98188847-98189505	K562	blood:	n/a	n/a
8	TEAD4	chr9:98188794-98189570	K562	blood:	n/a	n/a
9	E2F6	chr9:98188858-98189571	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:98188848-98189524	HCT-116	colon:	n/a	n/a
11	POLR2A	chr9:98188582-98189622	MCF-7	breast:	n/a	n/a
12	E2F6	chr9:98188249-98189608	A549	lung:	n/a	n/a
13	ELF1	chr9:98188901-98189545	MCF-7	breast:	n/a	chr9:98189215-98189228 chr9:98189191-98189204
14	POLR2A	chr9:98188879-98189468	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr9:98188438-98189508	A549	lung:	n/a	n/a
16	POLR2A	chr9:98188216-98189638	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr9:98188601-98189503	GM12892	blood:	n/a	n/a
18	SIN3AK20	chr9:98188822-98189590	MCF-7	breast:	n/a	n/a
19	RCOR1	chr9:98189001-98189684	K562	blood:	n/a	n/a
20	BHLHE40	chr9:98188530-98189598	K562	blood:	n/a	n/a
21	ATF2	chr9:98189088-98189467	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr9:98188854-98189539	Hela-S3	cervix:	n/a	n/a
23	MAX	chr9:98188846-98189576	ECC-1	luminal epithelium:	n/a	n/a
24	BHLHE40	chr9:98189121-98189488	A549	lung:	n/a	n/a
25	JUND	chr9:98188865-98189502	K562	blood:	n/a	chr9:98189370-98189381
26	POLR2A	chr9:98188733-98189531	K562	blood:	n/a	n/a
27	RAD21	chr9:98188938-98189527	A549	lung:	n/a	n/a
28	GABPA	chr9:98188870-98189592	MCF-7	breast:	n/a	n/a
29	CCNT2	chr9:98188856-98189479	K562	blood:	n/a	n/a
30	MYC	chr9:98188737-98189498	MCF10A-Er-Src	breast:	n/a	n/a
31	MYC	chr9:98188237-98189677	A549	lung:	n/a	n/a
32	MYC	chr9:98188492-98189525	K562	blood:	n/a	n/a
33	ZBTB7A	chr9:98188514-98189484	ECC-1	luminal epithelium:	n/a	chr9:98188523-98188537
34	MAX	chr9:98188824-98189531	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr9:98188700-98189588	ECC-1	luminal epithelium:	n/a	n/a
36	GABPA	chr9:98188736-98189560	A549	lung:	n/a	n/a
37	POLR2A	chr9:98188848-98189504	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr9:98188846-98189491	K562	blood:	n/a	n/a
39	ELF1	chr9:98188874-98189545	MCF-7	breast:	n/a	chr9:98189215-98189228 chr9:98189191-98189204
40	TAF1	chr9:98188559-98189564	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr9:98188842-98189525	ECC-1	luminal epithelium:	n/a	n/a
42	USF1	chr9:98189094-98189476	K562	blood:	n/a	n/a
43	POLR2A	chr9:98188767-98189467	ProgFib	skin:	n/a	n/a
44	POLR2A	chr9:98188736-98189516	PANC-1	pancreas:	n/a	n/a
45	TAF1	chr9:98188698-98189528	ECC-1	luminal epithelium:	n/a	n/a
46	NRF1	chr9:98189300-98189653	K562	blood:	n/a	chr9:98189494-98189505
47	POLR2A	chr9:98188124-98189524	HepG2	liver:	n/a	n/a
48	POLR2A	chr9:98188879-98189480	K562	blood:	n/a	n/a
49	SIN3AK20	chr9:98189117-98189506	A549	lung:	n/a	n/a
50	MYC	chr9:98188850-98189537	K562	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:98187644..98190286-chr9:98266151..98268622,2	K562	blood:
2	chr9:98187685..98192036-chr9:98266677..98274746,12	MCF-7	breast:
3	chr9:98189018..98191444-chr9:98246516..98248115,2	MCF-7	breast:
4	chr9:98186276..98191956-chr9:98269234..98276633,9	K562	blood:
5	chr9:98187259..98193172-chr9:98208629..98217669,12	MCF-7	breast:
6	chr9:98167871..98172268-chr9:98186784..98190412,5	MCF-7	breast:
7	chr9:98173730..98177988-chr9:98187520..98191004,5	K562	blood:
8	chr9:98173705..98177734-chr9:98187506..98190870,3	MCF-7	breast:
9	chr9:98187278..98190652-chr9:98265637..98273315,6	K562	blood:
10	chr9:98078552..98082181-chr9:98188850..98192317,4	MCF-7	breast:
11	chr9:98187335..98191305-chr9:98637767..98639481,3	MCF-7	breast:
12	chr10:14879889..14880461-chr9:98188785..98189543,2	HCT-116	colon:
13	chr9:98174491..98183187-chr9:98187141..98190074,10	K562	blood:
14	chr9:98188569..98190136-chr9:98266994..98268557,2	MCF-7	breast:
15	chr9:98188670..98189479-chr9:98637800..98638512,2	Hela-S3	cervix:
16	chr9:98187696..98190762-chr9:98268567..98271378,5	MCF-7	breast:
17	chr4:84456903..84457679-chr9:98188999..98189686,2	HCT-116	colon:
18	chr6:57182114..57182811-chr9:98189374..98189947,2	Hela-S3	cervix:
19	chr9:98188917..98190953-chr9:98637709..98639661,2	MCF-7	breast:
20	chr9:98171235..98175849-chr9:98186797..98190089,10	MCF-7	breast:
21	chr9:98170885..98173194-chr9:98189275..98191495,2	K562	blood:
22	chr12:52445014..52445648-chr9:98188994..98189705,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000237857	TF binding region
ENSG00000271384	Chromatin interaction
ENSG00000146143	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000187522	Chromatin interaction
ENSG00000213761	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000185267	Chromatin interaction
ENSG00000271659	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000175611	Chromatin interaction
ENSG00000138678	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10821464	0.83[AMR][1000 genomes]
rs10993534	0.90[ASW][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs12004780	0.85[JPT][hapmap]
rs2036514	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2404693	0.86[AMR][1000 genomes]
rs28471674	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28679639	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35041950	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35402806	0.86[AMR][1000 genomes]
rs35431736	0.84[AMR][1000 genomes]
rs357521	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs357552	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62558314	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6479605	0.84[AMR][1000 genomes]
rs7388704	0.90[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7868504	0.86[AMR][1000 genomes]
rs905615	0.86[AMR][1000 genomes]
rs913711	0.80[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes]
rs9695482	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1051731	chr9:98154815-98201115	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98187800-98190000	Active TSS	A549	lung
2	chr9:98188000-98189600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr9:98188000-98189600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr9:98188000-98189800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr9:98188200-98189600	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr9:98188200-98189800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:98188200-98189800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:98188200-98189800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:98188200-98190000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr9:98188400-98189600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr9:98188400-98189600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:98188400-98189600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:98188400-98189600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:98188400-98189600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:98188400-98189600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr9:98188400-98189600	Active TSS	Esophagus	oesophagus
17	chr9:98188400-98189600	Active TSS	Left Ventricle	heart
18	chr9:98188400-98189600	Active TSS	Pancreas	Pancrea
19	chr9:98188400-98189800	Active TSS	Rectal Smooth Muscle	rectum
20	chr9:98188400-98189800	Active TSS	Hela-S3	cervix
21	chr9:98188400-98189800	Active TSS	NHEK	skin
22	chr9:98188400-98190000	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr9:98188600-98189600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:98188600-98189600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:98188600-98189600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:98188600-98189600	Active TSS	Fetal Intestine Large	intestine
27	chr9:98188600-98189600	Active TSS	Psoas Muscle	Psoas
28	chr9:98188600-98189600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr9:98188600-98189600	Active TSS	Right Atrium	heart
30	chr9:98188600-98189800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr9:98188600-98189800	Active TSS	Colonic Mucosa	Colon
32	chr9:98188600-98189800	Active TSS	Fetal Kidney	kidney
33	chr9:98188600-98189800	Active TSS	HMEC	breast
34	chr9:98188800-98189600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr9:98188800-98189600	Active TSS	Brain Angular Gyrus	brain
36	chr9:98188800-98189600	Active TSS	Brain Anterior Caudate	brain
37	chr9:98188800-98189600	Active TSS	Fetal Lung	lung
38	chr9:98188800-98189600	Active TSS	Right Ventricle	heart
39	chr9:98188800-98189600	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr9:98188800-98189600	Active TSS	Stomach Smooth Muscle	stomach
41	chr9:98188800-98189600	Active TSS	HSMM	muscle
42	chr9:98188800-98189600	Active TSS	HSMMtube	muscle
43	chr9:98188800-98189600	Active TSS	NHLF	lung
44	chr9:98189000-98189600	Active TSS	Adipose Nuclei	Adipose
45	chr9:98189000-98189600	Active TSS	Brain Cingulate Gyrus	brain
46	chr9:98189000-98189600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr9:98189000-98189600	Active TSS	Placenta	Placenta
48	chr9:98189000-98189600	Active TSS	NH-A	brain
49	chr9:98189000-98189600	Active TSS	Osteobl	bone
50	chr9:98189000-98189800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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