Variant report

Variant	rs9869844
Chromosome Location	chr3:42623623-42623624
allele	A/C
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	TBP	chr3:42622832-42624255	K562	blood:	n/a	n/a
2	ELK1	chr3:42623335-42624107	K562	blood:	n/a	n/a
3	MAX	chr3:42622946-42624272	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:42622994-42624143	K562	blood:	n/a	n/a
5	BRCA1	chr3:42623000-42624347	Hela-S3	cervix:	n/a	n/a
6	ZBTB7A	chr3:42623564-42624124	K562	blood:	n/a	n/a
7	ATF3	chr3:42623403-42623992	K562	blood:	n/a	chr3:42623642-42623651
8	ELF1	chr3:42623013-42624035	GM12878	blood:	n/a	chr3:42623311-42623323 chr3:42623315-42623324
9	MBD4	chr3:42623484-42623943	HepG2	liver:	n/a	n/a
10	SP1	chr3:42623225-42624109	GM12878	blood:	n/a	chr3:42623787-42623801 chr3:42623485-42623499 chr3:42623791-42623800 chr3:42623484-42623495 chr3:42623792-42623801
11	TAF1	chr3:42623170-42623704	GM12878	blood:	n/a	n/a
12	FOXA1	chr3:42623258-42624302	T-47D	breast:	n/a	n/a
13	MAZ	chr3:42623147-42624151	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:42623169-42623828	A549	lung:	n/a	n/a
15	MAZ	chr3:42623014-42624137	K562	blood:	n/a	n/a
16	NRF1	chr3:42623260-42623807	Hela-S3	cervix:	n/a	chr3:42623459-42623473 chr3:42623438-42623449 chr3:42623464-42623473 chr3:42623462-42623473 chr3:42623462-42623473 chr3:42623318-42623327
17	POLR2A	chr3:42623033-42624113	K562	blood:	n/a	n/a
18	TFAP2A	chr3:42623217-42624106	Hela-S3	cervix:	n/a	chr3:42623826-42623834 chr3:42623826-42623834 chr3:42623826-42623834
19	MAX	chr3:42623320-42624002	SK-N-SH	brain:	n/a	n/a
20	SIN3AK20	chr3:42623313-42623972	HepG2	liver:	n/a	n/a
21	HDAC2	chr3:42623169-42624009	K562	blood:	n/a	chr3:42623464-42623473
22	ZNF143	chr3:42623107-42624108	GM12878	blood:	n/a	chr3:42623317-42623327 chr3:42623541-42623559
23	POLR2A	chr3:42622941-42624070	PFSK-1	brain:	n/a	n/a
24	REST	chr3:42623592-42624008	K562	blood:	n/a	n/a
25	POLR2A	chr3:42623109-42623928	A549	lung:	n/a	n/a
26	POLR2A	chr3:42623067-42624274	K562	blood:	n/a	n/a
27	SP4	chr3:42623249-42623913	H1-hESC	embryonic stem cell:	n/a	chr3:42623484-42623495
28	GTF2F1	chr3:42623232-42624031	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr3:42622971-42624164	GM18505	blood:	n/a	n/a
30	ATF3	chr3:42623255-42623994	K562	blood:	n/a	chr3:42623642-42623651
31	MAX	chr3:42622844-42624251	HepG2	liver:	n/a	n/a
32	SMC3	chr3:42623347-42624125	Hela-S3	cervix:	n/a	n/a
33	TAF1	chr3:42623004-42624189	H1-hESC	embryonic stem cell:	n/a	n/a
34	HCFC1	chr3:42622895-42624146	K562	blood:	n/a	n/a
35	GTF2B	chr3:42623157-42623970	K562	blood:	n/a	n/a
36	TAF1	chr3:42622981-42624083	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr3:42622962-42624103	Hela-S3	cervix:	n/a	n/a
38	CHD2	chr3:42623046-42624241	H1-hESC	embryonic stem cell:	n/a	chr3:42623489-42623499
39	POLR2A	chr3:42622990-42623980	HCT-116	colon:	n/a	n/a
40	KAP1	chr3:42622947-42624220	HEK293	kidney:	n/a	n/a
41	E2F4	chr3:42623431-42623928	GM12878	blood:	n/a	chr3:42623914-42623925 chr3:42623911-42623928 chr3:42623640-42623649 chr3:42623791-42623800 chr3:42623463-42623472 chr3:42623914-42623925 chr3:42623914-42623925 chr3:42623914-42623925 chr3:42623918-42623925
42	PML	chr3:42622828-42624097	K562	blood:	n/a	n/a
43	GATA2	chr3:42623477-42624420	SH-SY5Y	brain:	n/a	chr3:42623877-42623885
44	GATA3	chr3:42623440-42624415	T-47D	breast:	n/a	chr3:42623877-42623885
45	YY1	chr3:42623449-42623722	HCT-116	colon:	n/a	n/a
46	MXI1	chr3:42622689-42624175	Hela-S3	cervix:	n/a	n/a
47	UBTF	chr3:42622742-42624155	K562	blood:	n/a	n/a
48	POLR2A	chr3:42622846-42624133	GM18951	blood:	n/a	n/a
49	CBX3	chr3:42623149-42624201	K562	blood:	n/a	n/a
50	CTCF	chr3:42623532-42624128	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42623490..42624325-chr3:42676351..42677180,2	MCF-7	breast:
2	chr1:153599562..153600368-chr3:42622842..42623637,2	Hela-S3	cervix:
3	chr3:42623619..42624264-chr7:22862114..22862684,2	Hela-S3	cervix:
4	chr3:42622324..42624855-chr3:42675398..42677179,2	K562	blood:
5	chr3:42622045..42625365-chr3:42627615..42632564,8	MCF-7	breast:
6	chr10:90750277..90752970-chr3:42621806..42623827,2	MCF-7	breast:
7	chr11:61582239..61583475-chr3:42623325..42624365,3	Hela-S3	cervix:
8	chr17:56160432..56161286-chr3:42623181..42624002,2	Hela-S3	cervix:
9	chr22:22089770..22090272-chr3:42622964..42623955,2	Hela-S3	cervix:
10	chr3:42620803..42625287-chr3:42629964..42635186,7	MCF-7	breast:
11	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
12	chr3:42621283..42625330-chr3:42639303..42643596,7	MCF-7	breast:
13	chr3:42622208..42623993-chr3:42640628..42642693,2	MCF-7	breast:
14	chr3:42622951..42623830-chr6:34759784..34760772,2	Hela-S3	cervix:

Variant related genes	Relation type
SEC22C	TF binding region
ENSG00000100027	Chromatin interaction
ENSG00000264364	Chromatin interaction
ENSG00000149485	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000065060	Chromatin interaction
ENSG00000196683	Chromatin interaction
ENSG00000266290	Chromatin interaction
ENSG00000107796	Chromatin interaction
ENSG00000026103	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000222326	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000189171	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs9311325	1.00[AFR][1000 genomes]
rs9849556	0.88[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 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	chr3:42622000-42624600	Active TSS	A549	lung
2	chr3:42622200-42624000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:42622200-42624000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:42622400-42623800	Active TSS	Fetal Thymus	thymus
5	chr3:42622400-42624000	Active TSS	Fetal Brain Female	brain
6	chr3:42622400-42624200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:42622400-42624200	Active TSS	NHDF-Ad	bronchial
8	chr3:42622400-42624400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:42622400-42624400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:42622400-42624400	Active TSS	Brain Angular Gyrus	brain
11	chr3:42622400-42624600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:42622600-42623800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:42622600-42623800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:42622600-42623800	Active TSS	Fetal Muscle Leg	muscle
15	chr3:42622600-42623800	Active TSS	HMEC	breast
16	chr3:42622600-42624000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:42622600-42624000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:42622600-42624000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:42622600-42624000	Active TSS	Muscle Satellite Cultured Cells	--
20	chr3:42622600-42624000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:42622600-42624000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:42622600-42624000	Active TSS	Colon Smooth Muscle	Colon
23	chr3:42622600-42624000	Active TSS	Fetal Intestine Large	intestine
24	chr3:42622600-42624000	Active TSS	Thymus	Thymus
25	chr3:42622600-42624000	Active TSS	K562	blood
26	chr3:42622600-42624200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:42622600-42624200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:42622600-42624200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr3:42622600-42624200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr3:42622600-42624200	Active TSS	Right Ventricle	heart
31	chr3:42622600-42624400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:42622600-42624400	Active TSS	NHLF	lung
33	chr3:42622600-42624600	Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:42622600-42625000	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr3:42622600-42625200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:42622800-42623800	Active TSS	Fetal Brain Male	brain
37	chr3:42622800-42623800	Active TSS	Placenta	Placenta
38	chr3:42622800-42623800	Active TSS	HUVEC	blood vessel
39	chr3:42622800-42624000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:42622800-42624000	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr3:42622800-42624000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:42622800-42624000	Active TSS	Brain Cingulate Gyrus	brain
43	chr3:42622800-42624000	Active TSS	Duodenum Mucosa	Duodenum
44	chr3:42622800-42624000	Active TSS	Fetal Intestine Small	intestine
45	chr3:42622800-42624000	Active TSS	Pancreas	Pancrea
46	chr3:42622800-42624000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr3:42622800-42624000	Active TSS	Rectal Smooth Muscle	rectum
48	chr3:42622800-42624000	Active TSS	Hela-S3	cervix
49	chr3:42622800-42624000	Active TSS	HSMMtube	muscle
50	chr3:42622800-42624000	Active TSS	NH-A	brain

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