Variant report

Variant	rs9837291
Chromosome Location	chr3:196230564-196230565
allele	C/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	NFYB	chr3:196230386-196230794	GM12878	blood:	n/a	n/a
2	CHD2	chr3:196230428-196230705	HepG2	liver:	n/a	chr3:196230567-196230577
3	EP300	chr3:196230049-196230898	K562	blood:	n/a	chr3:196230720-196230727 chr3:196230421-196230437 chr3:196230736-196230745
4	STAT5A	chr3:196230294-196230816	K562	blood:	n/a	n/a
5	ZEB1	chr3:196230562-196230736	GM12878	blood:	n/a	n/a
6	RAD21	chr3:196230293-196230860	H1-hESC	embryonic stem cell:	n/a	chr3:196230421-196230434
7	USF1	chr3:196230407-196230878	ECC-1	luminal epithelium:	n/a	chr3:196230499-196230515
8	POLR2A	chr3:196229718-196231036	Raji	blood:	n/a	n/a
9	PBX3	chr3:196230330-196230928	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:196230123-196230874	H1-hESC	embryonic stem cell:	n/a	n/a
11	IRF1	chr3:196230229-196230808	K562	blood:	n/a	chr3:196230783-196230797
12	MAZ	chr3:196229283-196231121	IMR90	lung:	n/a	n/a
13	MAX	chr3:196229784-196230840	K562	blood:	n/a	n/a
14	CBX3	chr3:196230221-196230944	K562	blood:	n/a	n/a
15	CREB1	chr3:196229609-196231008	GM12878	blood:	n/a	n/a
16	FOXM1	chr3:196230231-196230957	MCF-7	breast:	n/a	n/a
17	USF2	chr3:196230502-196230713	Hela-S3	cervix:	n/a	n/a
18	REST	chr3:196230364-196230654	GM12878	blood:	n/a	n/a
19	HDAC2	chr3:196230345-196230981	MCF-7	breast:	n/a	n/a
20	EGR1	chr3:196230150-196230961	HCT-116	colon:	n/a	chr3:196230578-196230592 chr3:196230582-196230592 chr3:196230570-196230583 chr3:196230740-196230750 chr3:196230464-196230474 chr3:196230582-196230593 chr3:196230582-196230593
21	EBF1	chr3:196230348-196230797	GM12878	blood:	n/a	n/a
22	BATF	chr3:196230399-196230687	GM12878	blood:	n/a	n/a
23	ARID3A	chr3:196230433-196230722	K562	blood:	n/a	chr3:196230659-196230667
24	POLR2A	chr3:196229560-196231038	MCF10A-Er-Src	breast:	n/a	n/a
25	TAF1	chr3:196230389-196230642	PFSK-1	brain:	n/a	n/a
26	MAX	chr3:196229384-196230954	ECC-1	luminal epithelium:	n/a	n/a
27	EGR1	chr3:196230362-196230684	GM12878	blood:	n/a	chr3:196230578-196230592 chr3:196230582-196230592 chr3:196230570-196230583 chr3:196230464-196230474 chr3:196230582-196230593 chr3:196230582-196230593
28	HCFC1	chr3:196230290-196230910	K562	blood:	n/a	n/a
29	IRF4	chr3:196230176-196230668	GM12878	blood:	n/a	n/a
30	GTF2F1	chr3:196230409-196230707	K562	blood:	n/a	n/a
31	CREB1	chr3:196230269-196230995	ECC-1	luminal epithelium:	n/a	n/a
32	MAFK	chr3:196230452-196230652	K562	blood:	n/a	n/a
33	TCF12	chr3:196230403-196230707	A549	lung:	n/a	n/a
34	RFX5	chr3:196229552-196231300	Hela-S3	cervix:	n/a	n/a
35	STAT3	chr3:196230487-196230793	MCF10A-Er-Src	breast:	n/a	n/a
36	NFIC	chr3:196229404-196230988	ECC-1	luminal epithelium:	n/a	n/a
37	TAF1	chr3:196230128-196230872	K562	blood:	n/a	n/a
38	GABPA	chr3:196229653-196231133	MCF-7	breast:	n/a	chr3:196230569-196230578 chr3:196230736-196230745 chr3:196230489-196230496
39	MXI1	chr3:196229421-196230900	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:196230183-196230958	NB4	blood:	n/a	n/a
41	GABPA	chr3:196230371-196230823	GM12878	blood:	n/a	chr3:196230569-196230578 chr3:196230736-196230745 chr3:196230489-196230496
42	BRCA1	chr3:196230378-196230661	GM12878	blood:	n/a	n/a
43	GABPA	chr3:196230139-196231008	K562	blood:	n/a	chr3:196230569-196230578 chr3:196230736-196230745 chr3:196230489-196230496
44	POLR2A	chr3:196229648-196231278	HepG2	liver:	n/a	n/a
45	GATA3	chr3:196230275-196230929	T-47D	breast:	n/a	n/a
46	POLR2A	chr3:196229561-196230783	GM12891	blood:	n/a	n/a
47	HEY1	chr3:196230312-196230716	HepG2	liver:	n/a	chr3:196230615-196230630 chr3:196230609-196230624
48	STAT1	chr3:196229828-196230920	GM12878	blood:	n/a	chr3:196230878-196230889
49	SIN3AK20	chr3:196229410-196231010	MCF-7	breast:	n/a	n/a
50	MAFK	chr3:196229512-196230737	Hela-S3	cervix:	n/a	chr3:196229675-196229689 chr3:196229681-196229690

No.	Distal block	Cell Line	Cell type
1	chr3:196014537..196016415-chr3:196229117..196231929,2	MCF-7	breast:
2	chr3:196228328..196231500-chr3:196241253..196244010,3	MCF-7	breast:
3	chr3:195808495..195810108-chr3:196228997..196231874,2	K562	blood:
4	chr1:45187028..45187583-chr3:196230020..196230593,2	Hela-S3	cervix:
5	chr1:16840299..16840986-chr3:196230102..196230663,2	Hela-S3	cervix:
6	chr3:196062616..196065996-chr3:196228027..196230994,3	K562	blood:
7	chr3:195808373..195809995-chr3:196228997..196231632,2	K562	blood:
8	chr3:196228489..196231887-chr3:196292830..196296417,3	MCF-7	breast:
9	chr3:196156342..196159977-chr3:196227568..196231019,3	MCF-7	breast:
10	chr3:196228351..196232071-chr3:196294107..196297178,4	MCF-7	breast:
11	chr11:62608971..62609638-chr3:196230070..196230623,2	Hela-S3	cervix:
12	chr3:196064683..196067033-chr3:196229952..196232006,2	K562	blood:
13	chr3:196014550..196016725-chr3:196229110..196232092,4	K562	blood:

Variant related genes	Relation type
RNF168	TF binding region
ENSG00000214097	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000273331	Chromatin interaction
ENSG00000072274	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000185798	Chromatin interaction
ENSG00000161217	Chromatin interaction
ENSG00000174013	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13099664	0.87[ASN][1000 genomes]
rs34547573	0.90[ASN][1000 genomes]
rs7430950	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs9837568	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9844068	0.84[ASN][1000 genomes]
rs9869437	0.81[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	55 gene(s)	inside rSNPs	diseases
6	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
8	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr3:196225800-196231600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:196226400-196231000	Active TSS	GM12878-XiMat	blood
3	chr3:196226400-196231200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:196226800-196231200	Active TSS	Colonic Mucosa	Colon
5	chr3:196227000-196230800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:196227000-196231000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr3:196227000-196231000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:196227000-196231000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:196227000-196231000	Active TSS	Esophagus	oesophagus
10	chr3:196227000-196231200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr3:196227000-196231200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:196227000-196231200	Active TSS	Fetal Kidney	kidney
13	chr3:196227000-196231200	Active TSS	Rectal Smooth Muscle	rectum
14	chr3:196227200-196230600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr3:196227200-196230800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:196227200-196230800	Active TSS	Gastric	stomach
17	chr3:196227200-196231000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:196227200-196231000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:196227200-196231000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:196227200-196231000	Active TSS	Lung	lung
21	chr3:196227200-196231000	Active TSS	HMEC	breast
22	chr3:196227200-196231200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:196227200-196231200	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr3:196227200-196231200	Active TSS	Brain Angular Gyrus	brain
25	chr3:196227200-196231400	Active TSS	Fetal Muscle Trunk	muscle
26	chr3:196227200-196231600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:196227400-196230600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:196227400-196230600	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr3:196227400-196230600	Active TSS	Stomach Mucosa	stomach
30	chr3:196227400-196230800	Active TSS	Fetal Intestine Large	intestine
31	chr3:196227400-196230800	Active TSS	Dnd41	blood
32	chr3:196227400-196230800	Active TSS	NHEK	skin
33	chr3:196227400-196231000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:196227400-196231000	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr3:196227400-196231000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:196227400-196231000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:196227400-196231000	Active TSS	Aorta	Aorta
38	chr3:196227400-196231000	Active TSS	Colon Smooth Muscle	Colon
39	chr3:196227400-196231000	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr3:196227400-196231000	Active TSS	Fetal Brain Male	brain
41	chr3:196227400-196231000	Active TSS	Fetal Intestine Small	intestine
42	chr3:196227400-196231000	Active TSS	Fetal Lung	lung
43	chr3:196227400-196231000	Active TSS	Fetal Stomach	stomach
44	chr3:196227400-196231000	Active TSS	Ovary	ovary
45	chr3:196227400-196231000	Active TSS	A549	lung
46	chr3:196227400-196231000	Active TSS	Hela-S3	cervix
47	chr3:196227400-196231000	Active TSS	HSMM	muscle
48	chr3:196227400-196231000	Active TSS	HSMMtube	muscle
49	chr3:196227400-196231000	Active TSS	NHDF-Ad	bronchial
50	chr3:196227400-196231000	Active TSS	NHLF	lung

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