Variant report

Variant	rs56123740
Chromosome Location	chr9:86596863-86596864
allele	C/T
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	chr9:86593061-86596929	SK-N-MC	brain:	n/a	n/a
2	MAX	chr9:86593949-86596953	A549	lung:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
3	MYC	chr9:86596111-86596919	MCF10A-Er-Src	breast:	n/a	n/a
4	BACH1	chr9:86596582-86597119	K562	blood:	n/a	n/a
5	CEBPB	chr9:86596104-86596894	Hela-S3	cervix:	n/a	chr9:86596706-86596717
6	POLR2A	chr9:86592005-86597005	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
8	POLR2A	chr9:86589056-86597036	GM12878	blood:	n/a	n/a
9	RCOR1	chr9:86594122-86597693	K562	blood:	n/a	n/a
10	MAFK	chr9:86596397-86597394	K562	blood:	n/a	chr9:86596666-86596676 chr9:86597224-86597238 chr9:86596666-86596675 chr9:86597225-86597236 chr9:86597225-86597236
11	MYC	chr9:86594204-86597085	K562	blood:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
12	JUND	chr9:86594377-86597401	K562	blood:	n/a	chr9:86596666-86596678 chr9:86594436-86594445 chr9:86595324-86595338 chr9:86597230-86597239 chr9:86595271-86595280
13	IRF1	chr9:86596135-86597141	K562	blood:	n/a	n/a
14	POLR2A	chr9:86593185-86597118	GM12878	blood:	n/a	n/a
15	MAFK	chr9:86596449-86597346	IMR90	lung:	n/a	chr9:86596666-86596676 chr9:86597224-86597238 chr9:86596666-86596675 chr9:86597225-86597236 chr9:86597225-86597236
16	MYC	chr9:86593987-86596894	NB4	blood:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
17	POLR2A	chr9:86594087-86596878	K562	blood:	n/a	n/a
18	KAP1	chr9:86594334-86596877	HEK293	kidney:	n/a	n/a
19	MTA3	chr9:86593815-86597026	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr9:86593753-86596939	MCF-7	breast:	n/a	n/a
21	FOXA1	chr9:86596582-86597026	A549	lung:	n/a	chr9:86596827-86596842
22	MAFF	chr9:86596338-86597365	K562	blood:	n/a	n/a
23	E2F4	chr9:86594983-86597049	MCF10A-Er-Src	breast:	n/a	chr9:86595043-86595052 chr9:86595685-86595696 chr9:86595620-86595632 chr9:86595094-86595103 chr9:86595270-86595279 chr9:86595697-86595708 chr9:86595620-86595629 chr9:86597032-86597041 chr9:86595696-86595708 chr9:86595621-86595636
24	MYC	chr9:86594019-86596921	MCF10A-Er-Src	breast:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
25	MXI1	chr9:86596170-86597160	K562	blood:	n/a	n/a
26	POLR2A	chr9:86593722-86596959	GM12892	blood:	n/a	n/a
27	MXI1	chr9:86593530-86597131	IMR90	lung:	n/a	n/a
28	EP300	chr9:86596144-86597409	K562	blood:	n/a	n/a
29	FOXA2	chr9:86596719-86596903	HepG2	liver:	n/a	n/a
30	POLR2A	chr9:86596798-86596878	H1-hESC	embryonic stem cell:	n/a	n/a
31	EP300	chr9:86596236-86596909	GM12878	blood:	n/a	n/a
32	MAX	chr9:86594006-86596910	NB4	blood:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
33	POLR2A	chr9:86596684-86596866	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr9:86593808-86596918	MCF10A-Er-Src	breast:	n/a	n/a
35	REST	chr9:86593207-86597147	H1-neurons	neurons:	n/a	chr9:86595761-86595774 chr9:86596021-86596039 chr9:86594642-86594655
36	POLR2A	chr9:86594123-86596873	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr9:86593163-86597264	GM12891	blood:	n/a	n/a
38	EP300	chr9:86596260-86597430	GM12878	blood:	n/a	n/a
39	TBL1XR1	chr9:86596193-86597244	K562	blood:	n/a	n/a
40	CHD1	chr9:86592725-86596929	H1-hESC	embryonic stem cell:	n/a	chr9:86595578-86595587 chr9:86596056-86596066 chr9:86595550-86595560 chr9:86595273-86595283
41	CEBPB	chr9:86596103-86596880	K562	blood:	n/a	chr9:86596706-86596717
42	CUX1	chr9:86596581-86597284	K562	blood:	n/a	n/a
43	MYC	chr9:86594151-86597779	K562	blood:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
44	FOXA1	chr9:86596605-86596947	A549	lung:	n/a	chr9:86596827-86596842
45	NR3C1	chr9:86596643-86597021	A549	lung:	n/a	chr9:86597003-86597017 chr9:86596869-86596885
46	MAFK	chr9:86594217-86597217	Hela-S3	cervix:	n/a	chr9:86596666-86596676 chr9:86596666-86596675
47	POLR2A	chr9:86593848-86596873	HL-60	blood:	n/a	n/a
48	ZNF263	chr9:86593968-86596884	HEK293-T-REx	kidney:	n/a	n/a
49	MAZ	chr9:86596610-86597421	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86533979..86537502-chr9:86594012..86596999,11	MCF-7	breast:
2	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
3	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
4	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
5	chr9:86596431..86597964-chr9:86790384..86792267,2	MCF-7	breast:
6	chr9:86592736..86597542-chr9:86606160..86610925,6	K562	blood:
7	chr9:86533247..86537973-chr9:86593370..86597981,20	MCF-7	breast:

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

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs55952909	1.00[EUR][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

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86591800-86597000	Active TSS	Psoas Muscle	Psoas
2	chr9:86592200-86597000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:86592400-86597600	Active TSS	Fetal Brain Female	brain
4	chr9:86592600-86597000	Active TSS	Stomach Smooth Muscle	stomach
5	chr9:86592800-86597200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:86592800-86597200	Active TSS	NHLF	lung
7	chr9:86593000-86597000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:86593000-86597000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr9:86593000-86597200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:86593000-86597400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr9:86593000-86598600	Active TSS	GM12878-XiMat	blood
12	chr9:86593200-86597000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:86593200-86597000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:86593200-86597200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr9:86593600-86597200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr9:86594200-86598400	Active TSS	K562	blood
17	chr9:86594400-86597000	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr9:86594400-86597000	Active TSS	Dnd41	blood
19	chr9:86594400-86597200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:86594400-86597200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:86594400-86597200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr9:86594400-86597200	Active TSS	A549	lung
23	chr9:86594400-86597400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr9:86594600-86597200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:86595000-86597000	Active TSS	HepG2	liver
26	chr9:86595800-86597000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr9:86595800-86597200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:86596000-86597000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:86596000-86597200	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr9:86596200-86597000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:86596400-86597000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:86596400-86597000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:86596400-86597000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr9:86596400-86597000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:86596400-86597000	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr9:86596400-86597000	Flanking Active TSS	Fetal Stomach	stomach
37	chr9:86596400-86597000	Flanking Active TSS	Hela-S3	cervix
38	chr9:86596400-86597000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr9:86596400-86597200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:86596400-86597200	Flanking Active TSS	Fetal Heart	heart
41	chr9:86596400-86597200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr9:86596400-86597200	Flanking Active TSS	HUVEC	blood vessel
43	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
44	chr9:86596600-86597000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:86596600-86597000	Enhancers	Primary B cells from peripheral blood	blood
46	chr9:86596600-86597000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:86596600-86597000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:86596600-86597000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr9:86596600-86597000	Flanking Active TSS	Fetal Brain Male	brain
50	chr9:86596600-86597000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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