Variant report

Variant	rs62578854
Chromosome Location	chr9:117372425-117372426
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr9:117371661-117372429	GM12878	blood:	n/a	n/a
2	CEBPB	chr9:117372305-117372462	K562	blood:	n/a	n/a
3	ZNF384	chr9:117372000-117372454	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:117372060-117376570	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:117349336..117350972-chr9:117372211..117374265,2	MCF-7	breast:
2	chr9:117273026..117275791-chr9:117370242..117372713,2	MCF-7	breast:
3	chr9:117372326..117374917-chr9:117375396..117377851,3	K562	blood:
4	chr9:117348104..117352194-chr9:117371141..117379325,14	K562	blood:
5	chr9:117346757..117362857-chr9:117372020..117377914,21	MCF-7	breast:
6	chr9:117262731..117268447-chr9:117369704..117378306,14	K562	blood:
7	chr9:117346842..117352204-chr9:117370877..117374909,8	K562	blood:
8	chr9:117263907..117271703-chr9:117371218..117376768,10	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf91	TF binding region
ENSG00000095397	Chromatin interaction
ENSG00000136888	Chromatin interaction
ENSG00000201749	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10448251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817641	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982293	1.00[ASN][1000 genomes]
rs10982298	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982300	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982302	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982305	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982306	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982307	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982308	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982309	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982310	0.86[EUR][1000 genomes]
rs10982311	0.86[EUR][1000 genomes]
rs10982312	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982313	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982314	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982316	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982318	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982322	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982339	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982352	0.85[EUR][1000 genomes]
rs12005529	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12378786	1.00[ASN][1000 genomes]
rs12379017	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41278669	0.87[EUR][1000 genomes]
rs62578796	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578799	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578848	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578856	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578857	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578858	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579680	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579681	0.87[EUR][1000 genomes]
rs62579682	0.87[EUR][1000 genomes]
rs7019057	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043244	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73656153	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999009	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
2	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	157 gene(s)	inside rSNPs	diseases
6	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
19	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
20	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
21	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
22	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
23	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
24	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
25	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117356200-117373000	Weak transcription	Stomach Mucosa	stomach
2	chr9:117359000-117372600	Weak transcription	Colon Smooth Muscle	Colon
3	chr9:117360000-117373000	Weak transcription	Right Ventricle	heart
4	chr9:117360000-117373200	Weak transcription	Aorta	Aorta
5	chr9:117360800-117373400	Weak transcription	Small Intestine	intestine
6	chr9:117361200-117373000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:117361600-117372600	Weak transcription	Fetal Brain Male	brain
8	chr9:117361600-117372600	Weak transcription	Hela-S3	cervix
9	chr9:117361600-117372800	Weak transcription	Brain Angular Gyrus	brain
10	chr9:117361600-117372800	Weak transcription	Brain Anterior Caudate	brain
11	chr9:117361800-117372600	Weak transcription	K562	blood
12	chr9:117361800-117372800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:117361800-117373000	Weak transcription	Colonic Mucosa	Colon
14	chr9:117361800-117373200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:117362000-117372800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr9:117362200-117372800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:117362200-117372800	Weak transcription	Fetal Brain Female	brain
18	chr9:117362400-117372800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:117362600-117372800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:117362800-117373000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:117362800-117373000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:117363000-117372800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:117363000-117372800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:117363200-117372600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr9:117363400-117372600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:117363400-117372800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:117363400-117373200	Weak transcription	Gastric	stomach
28	chr9:117363400-117373400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:117363600-117372800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:117363600-117372800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr9:117363600-117372800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:117363600-117373200	Weak transcription	Lung	lung
33	chr9:117363800-117372600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:117363800-117372800	Weak transcription	Thymus	Thymus
35	chr9:117363800-117372800	Weak transcription	A549	lung
36	chr9:117363800-117373000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:117364200-117373200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:117364400-117372600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:117364400-117372600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:117364400-117372600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr9:117364400-117373000	Weak transcription	Fetal Intestine Small	intestine
42	chr9:117364400-117373200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:117364600-117372800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:117364600-117372800	Weak transcription	Spleen	Spleen
45	chr9:117364600-117373200	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:117364800-117372600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr9:117364800-117372600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr9:117365000-117372600	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:117365200-117372800	Weak transcription	Primary T cells from cord blood	blood
50	chr9:117365800-117372800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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