Variant report

Variant	rs73389036
Chromosome Location	chr9:6007551-6007552
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	MXI1	chr9:6006891-6007617	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr9:6007005-6008028	HEK293-T-REx	kidney:	n/a	chr9:6007056-6007065
3	CTCF	chr9:6007460-6007610	SK-N-SH_RA	brain:	n/a	n/a
4	MXI1	chr9:6006692-6008998	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr9:6006866-6007584	HUVEC	blood vessel:	n/a	n/a
6	HCFC1	chr9:6006627-6009015	Hela-S3	cervix:	n/a	n/a
7	TCF12	chr9:6006793-6007631	A549	lung:	n/a	n/a
8	EGR1	chr9:6007331-6007570	GM12878	blood:	n/a	chr9:6007444-6007458 chr9:6007484-6007498
9	CTCF	chr9:6007500-6007770	AG04449	skin:	n/a	n/a
10	YY1	chr9:6007529-6008704	HepG2	liver:	n/a	chr9:6008223-6008234 chr9:6008128-6008137 chr9:6008128-6008142 chr9:6008503-6008512 chr9:6008495-6008506 chr9:6007874-6007883
11	POLR2A	chr9:6007088-6008024	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:6006849-6008803	K562	blood:	n/a	n/a
13	POLR2A	chr9:6006851-6008935	NB4	blood:	n/a	n/a
14	MAX	chr9:6006924-6008855	GM12878	blood:	n/a	chr9:6008187-6008197 chr9:6007888-6007898 chr9:6007990-6008000 chr9:6008504-6008514
15	STAT5A	chr9:6007063-6007704	GM12878	blood:	n/a	n/a
16	MXI1	chr9:6006563-6008946	IMR90	lung:	n/a	n/a
17	MAX	chr9:6006718-6008783	K562	blood:	n/a	chr9:6008187-6008197 chr9:6007888-6007898 chr9:6007990-6008000 chr9:6008504-6008514
18	MAX	chr9:6006788-6008885	HepG2	liver:	n/a	chr9:6008187-6008197 chr9:6007888-6007898 chr9:6007990-6008000 chr9:6008504-6008514
19	SIN3AK20	chr9:6006860-6007749	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr9:6007460-6007610	HMF	breast:	n/a	n/a
21	BHLHE40	chr9:6006872-6008028	HepG2	liver:	n/a	n/a
22	POLR2A	chr9:6007072-6007636	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr9:6006945-6008896	GM18505	blood:	n/a	n/a
24	REST	chr9:6007012-6009114	H1-neurons	neurons:	n/a	chr9:6008408-6008418 chr9:6007110-6007123 chr9:6007039-6007052 chr9:6008083-6008093 chr9:6008164-6008174
25	CREB1	chr9:6006802-6008837	GM12878	blood:	n/a	n/a
26	MAX	chr9:6006657-6008774	A549	lung:	n/a	chr9:6008187-6008197 chr9:6007888-6007898 chr9:6007990-6008000 chr9:6008504-6008514
27	MXI1	chr9:6005845-6009194	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr9:6007480-6007630	GM12864	blood:	n/a	n/a
29	MAZ	chr9:6006870-6008859	K562	blood:	n/a	chr9:6008187-6008197 chr9:6007888-6007898 chr9:6007990-6008000 chr9:6008504-6008514
30	MYC	chr9:6007100-6008228	MCF-7	breast:	n/a	chr9:6008187-6008197 chr9:6007888-6007898 chr9:6007990-6008000
31	MAX	chr9:6006664-6008055	ECC-1	luminal epithelium:	n/a	chr9:6007888-6007898 chr9:6007990-6008000
32	CHD2	chr9:6006816-6008813	Hela-S3	cervix:	n/a	chr9:6008497-6008507 chr9:6008179-6008189 chr9:6007985-6007995
33	MAX	chr9:6006789-6007735	HepG2	liver:	n/a	n/a
34	EGR1	chr9:6007320-6007568	K562	blood:	n/a	chr9:6007444-6007458 chr9:6007484-6007498
35	MAX	chr9:6006720-6007648	ECC-1	luminal epithelium:	n/a	n/a
36	MYC	chr9:6006764-6008889	NB4	blood:	n/a	chr9:6008187-6008197 chr9:6007888-6007898 chr9:6007990-6008000 chr9:6008504-6008514
37	MXI1	chr9:6006787-6008904	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:6006956-6008928	HEK293	kidney:	n/a	n/a
39	POLR2A	chr9:6006981-6008786	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr9:6006891-6008921	GM12878	blood:	n/a	n/a
41	SIN3AK20	chr9:6006863-6007658	PFSK-1	brain:	n/a	n/a
42	HMGN3	chr9:6006746-6008478	K562	blood:	n/a	n/a
43	PML	chr9:6006689-6009001	GM12878	blood:	n/a	n/a
44	POLR2A	chr9:6007330-6007667	A549	lung:	n/a	n/a
45	SIN3A	chr9:6006871-6008736	GM12878	blood:	n/a	chr9:6008155-6008168 chr9:6007039-6007052
46	CTCF	chr9:6007460-6007610	HEK293	kidney:	n/a	n/a
47	SIN3AK20	chr9:6006931-6007705	A549	lung:	n/a	n/a
48	SIN3AK20	chr9:6006770-6007726	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr9:6006990-6008290	GM12891	blood:	n/a	n/a
50	E2F6	chr9:6006946-6008494	K562	blood:	n/a	chr9:6007962-6007971 chr9:6008088-6008097 chr9:6008262-6008274 chr9:6008473-6008482

No.	Distal block	Cell Line	Cell type
1	chr9:2015281..2016857-chr9:6006319..6008670,2	K562	blood:
2	chr9:5967488..5970171-chr9:6006384..6008559,2	K562	blood:
3	chr9:5827878..5830835-chr9:6005826..6008939,3	MCF-7	breast:
4	chr9:6006778..6010531-chr9:6011866..6018012,11	MCF-7	breast:

Variant related genes	Relation type
MIR4665	TF binding region
ENSG00000099219	Chromatin interaction
ENSG00000080503	Chromatin interaction
ENSG00000137040	Chromatin interaction
ENSG00000183354	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10116214	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975350	1.00[EUR][1000 genomes]
rs10975351	1.00[EUR][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975372	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975377	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	0.91[AMR][1000 genomes]
rs12337300	1.00[EUR][1000 genomes]
rs12337445	1.00[EUR][1000 genomes]
rs12337790	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339713	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339886	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339889	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340153	1.00[EUR][1000 genomes]
rs12340531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341021	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342166	1.00[EUR][1000 genomes]
rs12342282	1.00[EUR][1000 genomes]
rs12343325	1.00[EUR][1000 genomes]
rs12345849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351533	1.00[EUR][1000 genomes]
rs12352918	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1411949	1.00[EUR][1000 genomes]
rs1993912	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28431078	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs386775	1.00[EUR][1000 genomes]
rs57154492	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58291302	1.00[EUR][1000 genomes]
rs60037728	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes]
rs7029847	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383109	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383113	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383114	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383144	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73385128	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73387085	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73389044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397307	1.00[EUR][1000 genomes]
rs73397376	1.00[EUR][1000 genomes]
rs73399307	1.00[EUR][1000 genomes]
rs73639554	1.00[EUR][1000 genomes]
rs73639568	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853706	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7854980	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299025	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' 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	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 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	chr9:6005600-6009200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr9:6005800-6007600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:6005800-6009000	Active TSS	Ovary	ovary
4	chr9:6006000-6007600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr9:6006000-6007600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr9:6006000-6007800	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr9:6006000-6008800	Active TSS	NHDF-Ad	bronchial
8	chr9:6006000-6009000	Active TSS	Right Ventricle	heart
9	chr9:6006000-6009200	Active TSS	Psoas Muscle	Psoas
10	chr9:6006000-6009200	Active TSS	Right Atrium	heart
11	chr9:6006200-6007600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr9:6006200-6007600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:6006200-6007600	Flanking Active TSS	Liver	Liver
14	chr9:6006200-6008600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:6006200-6008600	Active TSS	HMEC	breast
16	chr9:6006200-6009000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:6006200-6009000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:6006200-6009200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr9:6006200-6009200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:6006200-6009200	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr9:6006200-6009200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:6006200-6009200	Active TSS	Fetal Thymus	thymus
23	chr9:6006200-6009400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr9:6006200-6009400	Active TSS	K562	blood
25	chr9:6006400-6007600	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr9:6006400-6007800	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr9:6006400-6008000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr9:6006400-6008800	Active TSS	Fetal Brain Female	brain
29	chr9:6006400-6008800	Active TSS	Stomach Smooth Muscle	stomach
30	chr9:6006400-6008800	Active TSS	GM12878-XiMat	blood
31	chr9:6006400-6009000	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr9:6006400-6009000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:6006400-6009000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:6006400-6009000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:6006400-6009400	Active TSS	HSMMtube	muscle
36	chr9:6006600-6007600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr9:6006600-6008600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr9:6006600-6008800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr9:6006600-6008800	Active TSS	A549	lung
40	chr9:6006600-6008800	Active TSS	Hela-S3	cervix
41	chr9:6006600-6008800	Active TSS	HSMM	muscle
42	chr9:6006600-6009000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr9:6006600-6009000	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr9:6006600-6009000	Active TSS	Brain Cingulate Gyrus	brain
45	chr9:6006600-6009000	Active TSS	Brain Hippocampus Middle	brain
46	chr9:6006600-6009200	Active TSS	H1 Cell Line	embryonic stem cell
47	chr9:6006600-6009200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:6006600-6009200	Active TSS	Brain Germinal Matrix	brain
49	chr9:6006600-6009200	Active TSS	Rectal Smooth Muscle	rectum
50	chr9:6006600-6009200	Active TSS	Thymus	Thymus

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