Variant report

Variant	rs28412122
Chromosome Location	chr9:98273791-98273792
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	E2F6	chr9:98273477-98274017	A549	lung:	n/a	chr9:98273817-98273826
2	USF2	chr9:98273672-98274050	H1-hESC	embryonic stem cell:	n/a	chr9:98273841-98273850 chr9:98273840-98273851 chr9:98273841-98273850
3	POLR2A	chr9:98273065-98273871	Gliobla	brain:	n/a	n/a
4	POLR2A	chr9:98272611-98274009	MCF10A-Er-Src	breast:	n/a	n/a
5	USF1	chr9:98272731-98274121	HCT-116	colon:	n/a	chr9:98273204-98273220 chr9:98273841-98273850 chr9:98273841-98273850 chr9:98273840-98273851
6	MXI1	chr9:98267312-98274672	IMR90	lung:	n/a	chr9:98273104-98273113 chr9:98269404-98269413
7	MYC	chr9:98272856-98274710	Hela-S3	cervix:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
8	MXI1	chr9:98272925-98274528	HepG2	liver:	n/a	chr9:98273104-98273113
9	POLR2A	chr9:98272978-98273920	GM15510	blood:	n/a	n/a
10	USF1	chr9:98273591-98274079	SK-N-SH_RA	brain:	n/a	chr9:98273841-98273850 chr9:98273841-98273850 chr9:98273840-98273851
11	NFIC	chr9:98273429-98273851	HepG2	liver:	n/a	n/a
12	MXI1	chr9:98272581-98274289	GM12878	blood:	n/a	chr9:98273104-98273113
13	TAF1	chr9:98272855-98273811	K562	blood:	n/a	n/a
14	RAD21	chr9:98273632-98274595	IMR90	lung:	n/a	n/a
15	JUND	chr9:98272933-98274800	K562	blood:	n/a	chr9:98274043-98274055
16	POLR2A	chr9:98272838-98274134	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr9:98273452-98274129	MCF-7	breast:	n/a	chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273839-98273854 chr9:98273844-98273852 chr9:98273839-98273852
18	PML	chr9:98273428-98274420	K562	blood:	n/a	n/a
19	JUN	chr9:98273639-98274860	K562	blood:	n/a	chr9:98274043-98274055
20	MYC	chr9:98273198-98273884	MCF-7	breast:	n/a	chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273839-98273854 chr9:98273844-98273852 chr9:98273839-98273852
21	BHLHE40	chr9:98272933-98274287	GM12878	blood:	n/a	chr9:98273204-98273220 chr9:98273841-98273850 chr9:98273841-98273850
22	HEY1	chr9:98272989-98274082	K562	blood:	n/a	n/a
23	MAX	chr9:98272488-98274201	A549	lung:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
24	SIN3A	chr9:98266518-98275316	H1-hESC	embryonic stem cell:	n/a	chr9:98268478-98268491 chr9:98273259-98273270 chr9:98273104-98273113 chr9:98271212-98271225 chr9:98270756-98270767 chr9:98271270-98271279 chr9:98272257-98272268 chr9:98273102-98273111 chr9:98271251-98271264
25	ZNF263	chr9:98272812-98274505	HEK293-T-REx	kidney:	n/a	chr9:98273070-98273079
26	SIN3A	chr9:98273667-98274030	GM12878	blood:	n/a	n/a
27	USF1	chr9:98273577-98274095	ECC-1	luminal epithelium:	n/a	chr9:98273841-98273850 chr9:98273841-98273850 chr9:98273840-98273851
28	MAX	chr9:98272737-98274583	SK-N-SH	brain:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
29	MYC	chr9:98273467-98273984	HUVEC	blood vessel:	n/a	chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273839-98273854 chr9:98273844-98273852 chr9:98273839-98273852
30	TFAP2C	chr9:98273197-98274429	Hela-S3	cervix:	n/a	chr9:98273855-98273870
31	MYBL2	chr9:98272952-98274080	HepG2	liver:	n/a	n/a
32	MXI1	chr9:98273565-98274541	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr9:98272686-98273898	GM19193	blood:	n/a	n/a
34	ZNF143	chr9:98272860-98273843	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYC	chr9:98273731-98274590	MCF10A-Er-Src	breast:	n/a	chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273839-98273854 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273839-98273852
36	ZNF384	chr9:98273497-98273879	K562	blood:	n/a	n/a
37	HEY1	chr9:98272980-98275121	K562	blood:	n/a	n/a
38	POLR2A	chr9:98273446-98273969	K562	blood:	n/a	n/a
39	MXI1	chr9:98273183-98274554	K562	blood:	n/a	n/a
40	TBL1XR1	chr9:98273631-98273934	GM12878	blood:	n/a	n/a
41	CTBP2	chr9:98273002-98273895	H1-hESC	embryonic stem cell:	n/a	n/a
42	ELF1	chr9:98273033-98273859	K562	blood:	n/a	n/a
43	USF1	chr9:98273622-98274015	A549	lung:	n/a	chr9:98273841-98273850 chr9:98273841-98273850 chr9:98273840-98273851
44	MYBL2	chr9:98273642-98274153	HepG2	liver:	n/a	n/a
45	TEAD4	chr9:98273528-98274139	K562	blood:	n/a	n/a
46	CHD2	chr9:98273195-98273813	K562	blood:	n/a	n/a
47	USF1	chr9:98273596-98274056	A549	lung:	n/a	chr9:98273841-98273850 chr9:98273841-98273850 chr9:98273840-98273851
48	POLR2A	chr9:98272689-98274423	HepG2	liver:	n/a	n/a
49	MAX	chr9:98272632-98274168	A549	lung:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
50	POLR2A	chr9:98272695-98273955	GM18526	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:98273384..98275933-chr9:98636308..98638563,2	K562	blood:
2	chr9:98272232..98274861-chr9:98331837..98334312,2	MCF-7	breast:
3	chr9:98255343..98257866-chr9:98273112..98275130,2	K562	blood:
4	chr12:48147118..48147716-chr9:98273193..98273921,2	Hela-S3	cervix:
5	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
6	chr9:98103672..98105349-chr9:98272991..98274766,2	K562	blood:
7	chr9:98079077..98082863-chr9:98272048..98274634,4	MCF-7	breast:
8	chr9:98172380..98174560-chr9:98273339..98275804,2	K562	blood:
9	chr9:98256366..98258410-chr9:98271924..98274612,2	K562	blood:
10	chr9:98218003..98222058-chr9:98271885..98274474,3	K562	blood:
11	chr9:98271289..98274209-chr9:98357697..98360375,2	MCF-7	breast:
12	chr9:98073533..98075085-chr9:98273778..98276270,2	K562	blood:
13	chr9:98187685..98192036-chr9:98266677..98274746,12	MCF-7	breast:
14	chr9:98186276..98191956-chr9:98269234..98276633,9	K562	blood:
15	chr9:98192901..98194795-chr9:98272389..98274432,2	K562	blood:
16	chr9:98268284..98270797-chr9:98272240..98274371,3	MCF-7	breast:
17	chr9:98104888..98106927-chr9:98272777..98274676,2	MCF-7	breast:
18	chr20:33865327..33866128-chr9:98273376..98274360,2	Hela-S3	cervix:
19	chr9:98078136..98081236-chr9:98271605..98275803,7	K562	blood:
20	chr9:98143874..98147656-chr9:98271045..98275159,6	MCF-7	breast:
21	chr9:98273168..98275933-chr9:98636308..98638563,3	K562	blood:
22	chr9:98227014..98229023-chr9:98271434..98274318,2	MCF-7	breast:
23	chr9:98270649..98275167-chr9:98636318..98639773,5	MCF-7	breast:
24	chr9:98010532..98014660-chr9:98272495..98275814,3	K562	blood:
25	chr11:72525497..72526111-chr9:98273232..98274211,2	Hela-S3	cervix:
26	chr9:98078212..98082706-chr9:98271985..98275473,10	K562	blood:
27	chr9:98272365..98275151-chr9:98293260..98296891,4	K562	blood:
28	chr9:98271686..98274631-chr9:98635342..98639467,4	MCF-7	breast:
29	chr9:98091823..98093994-chr9:98273200..98274710,2	MCF-7	breast:
30	chr9:98273303..98273822-chrX:153598030..153598632,2	NB4	blood:
31	chr3:38206679..38207231-chr9:98273294..98273922,2	Hela-S3	cervix:
32	chr9:97950616..97952464-chr9:98272435..98274822,2	K562	blood:
33	chr9:98265986..98270733-chr9:98272060..98274665,7	MCF-7	breast:
34	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000271659	TF binding region
ENSG00000172939	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000126005	Chromatin interaction
ENSG00000271314	Chromatin interaction
ENSG00000237857	Chromatin interaction
ENSG00000088298	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17368876	0.91[MEX][hapmap]
rs17369383	0.81[EUR][1000 genomes]
rs1877456	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066836	0.91[MEX][hapmap]
rs2274694	0.82[MEX][hapmap]
rs2297087	0.82[MEX][hapmap]
rs28394554	0.82[MEX][hapmap]
rs28410513	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28411363	0.81[EUR][1000 genomes]
rs28442014	0.82[MEX][hapmap]
rs28468571	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28485705	0.97[EUR][1000 genomes]
rs28488553	0.81[EUR][1000 genomes]
rs28491365	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504341	0.81[EUR][1000 genomes]
rs28702657	0.82[MEX][hapmap]
rs28704635	0.87[EUR][1000 genomes]
rs28705285	0.89[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3758301	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[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	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
2	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
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3421348	chr9:98272156-98274704	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	esv3424610	chr9:98272481-98274629	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98266600-98275000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr9:98267000-98274800	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr9:98267200-98274000	Active TSS	Fetal Intestine Large	intestine
4	chr9:98267200-98274200	Active TSS	Left Ventricle	heart
5	chr9:98267200-98274400	Active TSS	Ovary	ovary
6	chr9:98267400-98273800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:98267400-98273800	Active TSS	Fetal Intestine Small	intestine
8	chr9:98267400-98273800	Active TSS	Fetal Kidney	kidney
9	chr9:98267400-98273800	Active TSS	Small Intestine	intestine
10	chr9:98267400-98274000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr9:98267400-98274400	Active TSS	NHDF-Ad	bronchial
12	chr9:98267400-98274600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:98267400-98274800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:98267600-98274000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr9:98267600-98274000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr9:98267600-98274000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr9:98267600-98274000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:98267600-98274000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:98267600-98274000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:98267600-98274000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:98267600-98274000	Active TSS	Psoas Muscle	Psoas
22	chr9:98267600-98274200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:98267600-98274400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:98267600-98274400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:98267600-98274600	Active TSS	NHLF	lung
26	chr9:98267600-98274800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:98267800-98273800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:98267800-98273800	Active TSS	Duodenum Mucosa	Duodenum
29	chr9:98267800-98273800	Active TSS	HSMMtube	muscle
30	chr9:98267800-98274000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:98267800-98274000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:98267800-98274000	Active TSS	Placenta Amnion	Placenta Amnion
33	chr9:98267800-98274000	Active TSS	A549	lung
34	chr9:98267800-98274200	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr9:98267800-98274200	Active TSS	Aorta	Aorta
36	chr9:98267800-98274200	Active TSS	Brain Cingulate Gyrus	brain
37	chr9:98267800-98274200	Active TSS	Brain Hippocampus Middle	brain
38	chr9:98267800-98274200	Active TSS	Brain Substantia Nigra	brain
39	chr9:98267800-98274200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr9:98267800-98274200	Active TSS	Right Ventricle	heart
41	chr9:98267800-98274400	Active TSS	Pancreas	Pancrea
42	chr9:98267800-98274600	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr9:98267800-98274600	Active TSS	Brain Angular Gyrus	brain
44	chr9:98267800-98274600	Active TSS	Brain Anterior Caudate	brain
45	chr9:98267800-98274600	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr9:98267800-98274800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:98267800-98275000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:98268000-98273800	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr9:98268000-98274000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:98268000-98274000	Active TSS	Gastric	stomach

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