Variant report

Variant	rs9876107
Chromosome Location	chr3:143690208-143690209
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	E2F6	chr3:143690065-143690372	K562	blood:	n/a	n/a
2	ZBTB7A	chr3:143689675-143691051	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr3:143689636-143692179	H1-hESC	embryonic stem cell:	n/a	n/a
4	HDAC2	chr3:143689898-143692374	MCF-7	breast:	n/a	chr3:143690819-143690828 chr3:143690369-143690383
5	POLR2A	chr3:143689448-143692708	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:143689953-143692471	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:143689718-143692074	HEK293	kidney:	n/a	n/a
8	BACH1	chr3:143690053-143691021	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr3:143689428-143691555	H1-neurons	neurons:	n/a	chr3:143689885-143689905 chr3:143689912-143689925
10	TCF12	chr3:143690111-143691224	ECC-1	luminal epithelium:	n/a	n/a
11	EGR1	chr3:143690104-143690739	GM12878	blood:	n/a	chr3:143690541-143690554 chr3:143690619-143690629 chr3:143690625-143690635 chr3:143690540-143690555 chr3:143690541-143690554 chr3:143690621-143690634
12	IRF1	chr3:143690011-143691085	K562	blood:	n/a	chr3:143690567-143690584 chr3:143690412-143690429 chr3:143690250-143690264 chr3:143690616-143690630 chr3:143690412-143690424 chr3:143690602-143690616 chr3:143690483-143690494 chr3:143690180-143690194
13	TAF1	chr3:143690076-143690407	K562	blood:	n/a	n/a
14	TCF7L2	chr3:143689631-143692487	HCT-116	colon:	n/a	n/a
15	BRCA1	chr3:143689916-143691085	Hela-S3	cervix:	n/a	n/a
16	POU2F2	chr3:143690073-143690354	GM12891	blood:	n/a	n/a
17	MAX	chr3:143689475-143692453	A549	lung:	n/a	chr3:143689817-143689826 chr3:143689829-143689838 chr3:143689513-143689522
18	NFIC	chr3:143689875-143690940	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:143689516-143692415	HL-60	blood:	n/a	n/a
20	MAX	chr3:143689667-143692276	ECC-1	luminal epithelium:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
21	MYC	chr3:143689557-143692334	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
22	SRF	chr3:143689944-143691057	ECC-1	luminal epithelium:	n/a	chr3:143690277-143690292 chr3:143690276-143690294 chr3:143690274-143690292 chr3:143690280-143690294 chr3:143690278-143690291 chr3:143690278-143690289 chr3:143690280-143690289 chr3:143690276-143690290 chr3:143690279-143690296 chr3:143690276-143690293 chr3:143690279-143690290
23	POLR2A	chr3:143689882-143692298	MCF-7	breast:	n/a	n/a
24	FOXM1	chr3:143689578-143692479	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:143689635-143692573	GM12878	blood:	n/a	n/a
26	CEBPB	chr3:143690163-143690586	IMR90	lung:	n/a	n/a
27	NFIC	chr3:143690125-143691170	ECC-1	luminal epithelium:	n/a	n/a
28	CTCF	chr3:143690080-143690230	HRE	kidney:	n/a	n/a
29	MAX	chr3:143689459-143692886	Hela-S3	cervix:	n/a	chr3:143689817-143689826 chr3:143689829-143689838 chr3:143689513-143689522
30	POLR2A	chr3:143689651-143692557	GM18526	blood:	n/a	n/a
31	MYC	chr3:143689633-143692296	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
32	MAX	chr3:143689528-143692416	HCT-116	colon:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
33	POLR2A	chr3:143689924-143691808	A549	lung:	n/a	n/a
34	CTCF	chr3:143689842-143690495	K562	blood:	n/a	n/a
35	POLR2A	chr3:143689670-143692495	GM15510	blood:	n/a	n/a
36	CUX1	chr3:143689941-143690461	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:143689852-143691849	GM12878	blood:	n/a	n/a
38	MXI1	chr3:143689654-143692425	GM12878	blood:	n/a	chr3:143689823-143689838 chr3:143689811-143689826
39	MAX	chr3:143689675-143691869	A549	lung:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
40	POLR2A	chr3:143689898-143692254	MCF-7	breast:	n/a	n/a
41	ELF1	chr3:143690006-143691105	MCF-7	breast:	n/a	chr3:143691041-143691053 chr3:143690785-143690797
42	RUNX3	chr3:143689706-143692538	GM12878	blood:	n/a	chr3:143690436-143690445 chr3:143690436-143690445 chr3:143690482-143690497
43	CTCF	chr3:143690180-143690330	HAc	cerebellar:	n/a	n/a
44	CREB1	chr3:143689619-143691129	H1-hESC	embryonic stem cell:	n/a	n/a
45	MXI1	chr3:143689589-143692923	Hela-S3	cervix:	n/a	chr3:143689823-143689838 chr3:143689811-143689826 chr3:143689595-143689604
46	MYC	chr3:143690108-143690390	MCF-7	breast:	n/a	n/a
47	MYC	chr3:143689554-143692333	NB4	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
48	SIN3AK20	chr3:143689603-143691944	MCF-7	breast:	n/a	n/a
49	NFATC1	chr3:143690179-143691086	GM12878	blood:	n/a	n/a
50	FOSL2	chr3:143690148-143690707	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:143690208-143690258	GM12891	blood:	n/a
2	chr3:143690208-143690258	SKMC	muscle:	n/a
3	chr3:143690208-143690258	GM12892	blood:	n/a
4	chr3:143690208-143690258	RPTEC	kidney:	n/a
5	chr3:143690208-143690258	ovcar-3	ovarian:	n/a
6	chr3:143690208-143690258	AG10803	skin:	n/a
7	chr3:143690208-143690258	AG04449	skin:	fetal
8	chr3:143690208-143690258	HL-60	blood:	n/a
9	chr3:143690208-143690258	NB4	blood:	n/a
10	chr3:143690208-143690258	AG09319	gingival:	n/a
11	chr3:143690208-143690258	SK-N-MC	brain:	n/a
12	chr3:143690208-143690258	AG09309	skin:	n/a
13	chr3:143690208-143690258	HPAEpiC	pulmonary alveolar:	n/a
14	chr3:143690208-143690258	HEEpiC	esophagus:	n/a
15	chr3:143690208-143690258	HUVEC	blood vessel:	n/a
16	chr3:143690208-143690258	NT2-D1	testis:	n/a
17	chr3:143690208-143690258	HMEC	breast:	n/a
18	chr3:143690208-143690258	K562	blood:	n/a
19	chr3:143690208-143690258	HCPEpiC	choroid plexus:	n/a
20	chr3:143690208-143690258	NH-A	brain:	n/a
21	chr3:143690208-143690258	SK-N-SH_RA	brain:	n/a
22	chr3:143690208-143690258	NHDF-neo	bronchial:	n/a
23	chr3:143690208-143690258	HIPEpiC	eye:	n/a
24	chr3:143690208-143690258	BE2_C	brain:	n/a
25	chr3:143690208-143690258	PrEC	prostate:	n/a
26	chr3:143690208-143690258	ProgFib	skin:	n/a
27	chr3:143690208-143690258	HRE	kidney:	n/a
28	chr3:143690208-143690258	HRCEpiC	kidney:	n/a
29	chr3:143690208-143690258	HCF	heart:	n/a
30	chr3:143690208-143690258	HEK293	kidney:	embryo
31	chr3:143690208-143690258	AG04450	lung:	fetal
32	chr3:143690208-143690258	Hepatocyte	liver:	n/a
33	chr3:143690208-143690258	HNPCEpiC	eye:	n/a
34	chr3:143690208-143690258	SK-N-SH	brain:	n/a
35	chr3:143690208-143690258	H1-hESC	embryonic stem cell:	embryo
36	chr3:143690208-143690258	HCT-116	colon:	n/a
37	chr3:143690208-143690258	A549	lung:	n/a
38	chr3:143690208-143690258	Caco-2	colon:	n/a
39	chr3:143690208-143690258	SAEC	small airway:	n/a
40	chr3:143690208-143690258	Jurkat	blood:	n/a
41	chr3:143690208-143690258	BJ	skin:	n/a
42	chr3:143690208-143690258	PANC-1	pancreas:	n/a
43	chr3:143690208-143690258	LNCaP	prostate:	n/a
44	chr3:143690208-143690258	U87	brain:	n/a
45	chr3:143690208-143690258	HRPEpiC	eye:	n/a
46	chr3:143690208-143690258	Hela-S3	cervix:	n/a
47	chr3:143690208-143690258	T-47D	breast:	n/a
48	chr3:143690208-143690258	GM06990	blood:	n/a
49	chr3:143690208-143690258	HepG2	liver:	n/a
50	chr3:143690208-143690258	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:143689958..143690542-chr6:44224790..44225315,2	Hela-S3	cervix:
2	chr22:19418740..19420583-chr3:143689830..143691587,2	MCF-7	breast:
3	chr11:17097769..17100478-chr3:143690055..143692307,2	MCF-7	breast:
4	chr3:143689763..143690371-chr7:23510326..23510860,2	Hela-S3	cervix:
5	chr19:44258720..44259380-chr3:143690069..143691057,2	Hela-S3	cervix:
6	chr12:12956339..12957122-chr3:143689535..143690489,2	Hela-S3	cervix:
7	chr3:143688929..143690453-chr9:116724811..116727064,2	MCF-7	breast:
8	chr17:57914617..57916585-chr3:143689584..143691332,2	MCF-7	breast:
9	chr3:143689777..143690496-chr6:26055384..26056279,2	Hela-S3	cervix:

Variant related genes	Relation type
C3orf58	TF binding region
C3orf58	CpG island
ENSG00000062716	Chromatin interaction
ENSG00000185608	Chromatin interaction
ENSG00000100084	Chromatin interaction
ENSG00000110700	Chromatin interaction
ENSG00000157593	Chromatin interaction
ENSG00000105771	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11720435	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11917772	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13317365	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13320111	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1604886	0.88[EUR][1000 genomes]
rs2370173	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28627639	0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56880774	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6776760	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73000690	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73872672	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637012	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs964572	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9823162	0.85[AMR][1000 genomes]
rs9834740	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9835993	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9847681	0.85[AMR][1000 genomes]
rs9849618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9860540	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866992	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9870939	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9874033	0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9879081	0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3349108	chr3:143676303-143692796	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 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	chr3:143688800-143696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:143689000-143693200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:143689000-143694400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:143689000-143695400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:143689000-143696800	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:143689200-143693200	Active TSS	A549	lung
7	chr3:143689200-143693400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:143689200-143693800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:143689200-143694400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:143689200-143695400	Active TSS	K562	blood
11	chr3:143689200-143695800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:143689200-143696200	Active TSS	GM12878-XiMat	blood
13	chr3:143689400-143690600	Active TSS	Brain Germinal Matrix	brain
14	chr3:143689400-143691000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:143689400-143691200	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr3:143689400-143691400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:143689400-143692000	Active TSS	Placenta	Placenta
18	chr3:143689400-143692400	Active TSS	Primary T cells from cord blood	blood
19	chr3:143689400-143692400	Active TSS	Duodenum Mucosa	Duodenum
20	chr3:143689400-143692600	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr3:143689400-143693000	Active TSS	Fetal Kidney	kidney
22	chr3:143689400-143693200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr3:143689400-143693200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:143689400-143693200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:143689400-143693200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:143689400-143693200	Active TSS	Stomach Mucosa	stomach
27	chr3:143689400-143693400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:143689400-143693400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:143689400-143693400	Active TSS	Colon Smooth Muscle	Colon
30	chr3:143689400-143693400	Active TSS	Psoas Muscle	Psoas
31	chr3:143689400-143693400	Active TSS	Right Ventricle	heart
32	chr3:143689400-143693600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:143689400-143693600	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr3:143689400-143693600	Active TSS	Fetal Muscle Trunk	muscle
35	chr3:143689400-143693600	Active TSS	Rectal Smooth Muscle	rectum
36	chr3:143689400-143693600	Active TSS	Thymus	Thymus
37	chr3:143689400-143693600	Active TSS	NHDF-Ad	bronchial
38	chr3:143689400-143693800	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr3:143689400-143693800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:143689400-143694000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:143689400-143694000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:143689400-143694000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr3:143689400-143694000	Active TSS	Fetal Thymus	thymus
44	chr3:143689400-143694200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:143689400-143694200	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr3:143689400-143694200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:143689400-143694400	Active TSS	H1 Cell Line	embryonic stem cell
48	chr3:143689400-143694400	Active TSS	Fetal Muscle Leg	muscle
49	chr3:143689400-143694800	Active TSS	Brain Anterior Caudate	brain
50	chr3:143689400-143695000	Active TSS	Brain Hippocampus Middle	brain

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