Variant report

Variant	rs796004
Chromosome Location	chr9:86594798-86594799
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	POLR2A	chr9:86593844-86596744	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr9:86594278-86595948	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:86593922-86596698	K562	blood:	n/a	n/a
4	POLR2A	chr9:86594364-86595834	A549	lung:	n/a	n/a
5	PBX3	chr9:86594236-86596215	SK-N-SH	brain:	n/a	chr9:86595226-86595246
6	SP1	chr9:86594287-86596067	A549	lung:	n/a	chr9:86595268-86595280 chr9:86595270-86595279 chr9:86595147-86595161 chr9:86595871-86595881 chr9:86595871-86595880 chr9:86595621-86595630 chr9:86594928-86594937 chr9:86594434-86594448 chr9:86594595-86594609 chr9:86595620-86595629 chr9:86594434-86594443 chr9:86595547-86595561 chr9:86594927-86594939 chr9:86594737-86594746 chr9:86595872-86595881 chr9:86595871-86595880 chr9:86594596-86594605 chr9:86595665-86595679 chr9:86595550-86595562 chr9:86595616-86595630 chr9:86595872-86595885 chr9:86595142-86595151 chr9:86595551-86595560 chr9:86595552-86595561 chr9:86595269-86595278 chr9:86595269-86595279 chr9:86594430-86594439 chr9:86595621-86595630 chr9:86595551-86595561 chr9:86595550-86595562 chr9:86594435-86594444 chr9:86594924-86594938 chr9:86595619-86595631 chr9:86595140-86595152 chr9:86594594-86594606 chr9:86595269-86595283
7	SMC3	chr9:86594364-86595080	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:86593958-86596248	K562	blood:	n/a	n/a
9	YY1	chr9:86594278-86595907	K562	blood:	n/a	chr9:86595086-86595097 chr9:86594539-86594549 chr9:86594914-86594924 chr9:86594533-86594550 chr9:86595094-86595103 chr9:86595620-86595629 chr9:86595140-86595151
10	IRF1	chr9:86594272-86595912	K562	blood:	n/a	chr9:86594484-86594495 chr9:86594483-86594495 chr9:86594484-86594498 chr9:86595182-86595191 chr9:86594431-86594445 chr9:86595619-86595633 chr9:86594480-86594494
11	PML	chr9:86594292-86596039	K562	blood:	n/a	n/a
12	POLR2A	chr9:86593110-86595750	A549	lung:	n/a	n/a
13	ZKSCAN1	chr9:86594769-86596644	Hela-S3	cervix:	n/a	n/a
14	ATF1	chr9:86594482-86595795	K562	blood:	n/a	n/a
15	MXI1	chr9:86593619-86596557	Hela-S3	cervix:	n/a	n/a
16	MAX	chr9:86594290-86595872	HUVEC	blood vessel:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
17	HEY1	chr9:86593873-86596014	HepG2	liver:	n/a	chr9:86595085-86595100 chr9:86595677-86595692
18	POLR2A	chr9:86594111-86596658	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr9:86593061-86596929	SK-N-MC	brain:	n/a	n/a
20	MAX	chr9:86593949-86596953	A549	lung:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
21	POU2F2	chr9:86594783-86595726	GM12878	blood:	n/a	chr9:86595270-86595282 chr9:86595617-86595629 chr9:86594922-86594934 chr9:86595547-86595559
22	NFIC	chr9:86594230-86594890	HepG2	liver:	n/a	n/a
23	ATF2	chr9:86594095-86595833	H1-hESC	embryonic stem cell:	n/a	n/a
24	FOXM1	chr9:86594256-86595997	GM12878	blood:	n/a	n/a
25	BCL3	chr9:86594199-86595879	A549	lung:	n/a	chr9:86595732-86595741 chr9:86595085-86595094 chr9:86594760-86594769 chr9:86595086-86595099
26	MAX	chr9:86594346-86596530	SK-N-SH	brain:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
27	POLR2A	chr9:86594012-86596039	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr9:86593882-86596480	GM12891	blood:	n/a	n/a
29	TCF12	chr9:86594247-86596222	MCF-7	breast:	n/a	chr9:86596024-86596031 chr9:86594510-86594517 chr9:86596020-86596030
30	TAF1	chr9:86594143-86596210	A549	lung:	n/a	n/a
31	PBX3	chr9:86594197-86596105	SK-N-SH	brain:	n/a	chr9:86595226-86595246
32	YY1	chr9:86594798-86594987	HCT-116	colon:	n/a	chr9:86594914-86594924
33	RELA	chr9:86594040-86596640	GM18951	blood:	n/a	n/a
34	POLR2A	chr9:86593956-86596774	H1-neurons	neurons:	n/a	n/a
35	PML	chr9:86594764-86595967	GM12878	blood:	n/a	n/a
36	POLR2A	chr9:86593527-86596747	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:86592005-86597005	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF7	chr9:86594338-86596194	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF1	chr9:86594310-86596486	ECC-1	luminal epithelium:	n/a	n/a
40	ETS1	chr9:86594180-86595753	K562	blood:	n/a	chr9:86595578-86595587 chr9:86595142-86595153 chr9:86595618-86595629 chr9:86594233-86594242 chr9:86594926-86594937 chr9:86594596-86594607 chr9:86594535-86594549
41	ELF1	chr9:86594259-86596166	GM12878	blood:	n/a	chr9:86595096-86595108 chr9:86596008-86596020 chr9:86595089-86595098 chr9:86596051-86596063
42	YY1	chr9:86594283-86595791	GM12891	blood:	n/a	chr9:86595086-86595097 chr9:86594539-86594549 chr9:86594914-86594924 chr9:86594533-86594550 chr9:86595094-86595103 chr9:86595620-86595629 chr9:86595140-86595151
43	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
44	TRIM28	chr9:86594260-86595932	K562	blood:	n/a	n/a
45	TBP	chr9:86594213-86595870	HepG2	liver:	n/a	n/a
46	FOXM1	chr9:86594172-86596248	GM12878	blood:	n/a	n/a
47	POLR2A	chr9:86589056-86597036	GM12878	blood:	n/a	n/a
48	POLR2A	chr9:86594240-86596078	Gliobla	brain:	n/a	n/a
49	POLR2A	chr9:86593589-86596833	GM12892	blood:	n/a	n/a
50	EP300	chr9:86594293-86595958	SK-N-SH	brain:	n/a	chr9:86595043-86595059 chr9:86595713-86595727

No.	Distal block	Cell Line	Cell type
1	chr9:86533979..86537502-chr9:86594012..86596999,11	MCF-7	breast:
2	chr11:62432743..62434322-chr9:86593092..86595353,2	MCF-7	breast:
3	chr17:80250206..80251061-chr9:86594587..86595234,2	Hela-S3	cervix:
4	chr10:38145904..38148087-chr9:86593901..86595485,2	MCF-7	breast:
5	chr20:30192630..30193506-chr9:86594310..86595123,2	Hela-S3	cervix:
6	chr16:776639..778399-chr9:86594223..86596178,2	MCF-7	breast:
7	chr6:33359301..33359882-chr9:86594730..86595587,2	Hela-S3	cervix:
8	chr5:133560806..133561386-chr9:86594639..86595588,2	Hela-S3	cervix:
9	chr18:12376849..12377806-chr9:86594670..86595620,2	Hela-S3	cervix:
10	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
11	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
12	chr12:77272410..77273249-chr9:86594788..86595326,2	Hela-S3	cervix:
13	chr10:43931809..43932733-chr9:86594490..86595462,2	Hela-S3	cervix:
14	chr9:86593378..86594996-chr9:86858039..86859653,2	MCF-7	breast:
15	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
16	chr17:57914983..57917065-chr9:86592190..86594994,2	MCF-7	breast:
17	chr9:86594678..86596625-chr9:86954974..86956986,2	MCF-7	breast:
18	chr9:86534520..86537940-chr9:86592614..86595774,6	K562	blood:
19	chr11:8703786..8704731-chr9:86594490..86595278,2	Hela-S3	cervix:
20	chr9:86593375..86596264-chr9:101558546..101560057,2	MCF-7	breast:
21	chr3:14988158..14990908-chr9:86594139..86596513,2	MCF-7	breast:
22	chr9:86592736..86597542-chr9:86606160..86610925,6	K562	blood:
23	chr8:53372582..53373541-chr9:86594741..86595608,2	Hela-S3	cervix:
24	chr9:86593982..86596635-chr9:88968626..88970254,2	MCF-7	breast:
25	chr9:86533247..86537973-chr9:86593370..86597981,20	MCF-7	breast:
26	chr12:56510343..56511008-chr9:86594409..86595109,2	Hela-S3	cervix:
27	chr4:56412226..56412922-chr9:86594760..86595405,2	HCT-116	colon:
28	chr15:44828332..44829115-chr9:86594438..86595354,2	Hela-S3	cervix:
29	chr11:62609023..62610551-chr9:86593862..86596703,2	MCF-7	breast:

Variant related genes	Relation type
HNRNPK	TF binding region
RMI1	TF binding region
ENSG00000206597	Chromatin interaction
ENSG00000177463	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000225733	Chromatin interaction
ENSG00000162004	Chromatin interaction
ENSG00000236514	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000265692	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000179523	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000197506	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000083223	Chromatin interaction
ENSG00000243660	Chromatin interaction
ENSG00000202523	Chromatin interaction
ENSG00000113575	Chromatin interaction
ENSG00000147488	Chromatin interaction
ENSG00000165138	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000103253	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000198105	Chromatin interaction
ENSG00000175183	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10114889	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10115699	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10125715	0.82[ASN][1000 genomes]
rs10868068	0.81[EUR][1000 genomes]
rs10868070	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10868071	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10868076	0.98[ASN][1000 genomes]
rs10868080	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140289	0.83[EUR][1000 genomes]
rs13296528	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs167203	0.81[EUR][1000 genomes]
rs1831757	0.82[EUR][1000 genomes]
rs1889113	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1982151	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2576362	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2780103	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296883	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs296886	0.81[EUR][1000 genomes]
rs296887	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296888	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296890	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818725	0.86[ASN][1000 genomes]
rs4147132	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4147133	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4535826	0.91[ASN][1000 genomes]
rs6559751	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6559752	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs696825	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7020300	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7033292	0.84[EUR][1000 genomes]
rs7045126	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7853254	0.86[EUR][1000 genomes]
rs796003	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796007	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs796004	HNRNPK,MIR7-1	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86591600-86596600	Active TSS	Ovary	ovary
2	chr9:86591800-86597000	Active TSS	Psoas Muscle	Psoas
3	chr9:86592200-86596800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:86592200-86597000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:86592400-86596200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr9:86592400-86596400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:86592400-86596600	Active TSS	Aorta	Aorta
8	chr9:86592400-86596800	Active TSS	Right Ventricle	heart
9	chr9:86592400-86597600	Active TSS	Fetal Brain Female	brain
10	chr9:86592600-86596200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:86592600-86596400	Active TSS	HSMMtube	muscle
12	chr9:86592600-86596600	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr9:86592600-86596600	Active TSS	Thymus	Thymus
14	chr9:86592600-86596800	Active TSS	Right Atrium	heart
15	chr9:86592600-86597000	Active TSS	Stomach Smooth Muscle	stomach
16	chr9:86592800-86595000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
17	chr9:86592800-86595400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:86592800-86596400	Active TSS	Fetal Muscle Leg	muscle
19	chr9:86592800-86596400	Active TSS	Placenta Amnion	Placenta Amnion
20	chr9:86592800-86596400	Active TSS	HMEC	breast
21	chr9:86592800-86596600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr9:86592800-86596600	Active TSS	Fetal Intestine Large	intestine
23	chr9:86592800-86596600	Active TSS	Fetal Intestine Small	intestine
24	chr9:86592800-86596800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:86592800-86597200	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr9:86592800-86597200	Active TSS	NHLF	lung
27	chr9:86593000-86596200	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr9:86593000-86596400	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr9:86593000-86596400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:86593000-86596400	Active TSS	Brain Angular Gyrus	brain
31	chr9:86593000-86596400	Active TSS	Brain Anterior Caudate	brain
32	chr9:86593000-86596400	Active TSS	Brain Cingulate Gyrus	brain
33	chr9:86593000-86596400	Active TSS	Brain Hippocampus Middle	brain
34	chr9:86593000-86596400	Active TSS	Colon Smooth Muscle	Colon
35	chr9:86593000-86596400	Active TSS	Fetal Stomach	stomach
36	chr9:86593000-86596400	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr9:86593000-86596400	Active TSS	Rectal Smooth Muscle	rectum
38	chr9:86593000-86596400	Active TSS	Hela-S3	cervix
39	chr9:86593000-86596400	Active TSS	HUVEC	blood vessel
40	chr9:86593000-86596400	Active TSS	NH-A	brain
41	chr9:86593000-86596600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr9:86593000-86596600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:86593000-86596600	Active TSS	Duodenum Mucosa	Duodenum
44	chr9:86593000-86596600	Active TSS	Fetal Kidney	kidney
45	chr9:86593000-86596800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:86593000-86596800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:86593000-86596800	Active TSS	Fetal Thymus	thymus
48	chr9:86593000-86596800	Active TSS	HSMM	muscle
49	chr9:86593000-86596800	Active TSS	NHDF-Ad	bronchial
50	chr9:86593000-86597000	Active TSS	H9 Cell Line	embryonic stem cell

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