Variant report

Variant	rs11578802
Chromosome Location	chr1:92197677-92197678
allele	A/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	MTA3	chr1:92197327-92198423	GM12878	blood:	n/a	n/a
2	TCF7L2	chr1:92197343-92198456	PANC-1	pancreas:	n/a	chr1:92198242-92198251
3	RUNX3	chr1:92197296-92198408	GM12878	blood:	n/a	chr1:92197576-92197585 chr1:92197576-92197585
4	SMC3	chr1:92197395-92198452	Hela-S3	cervix:	n/a	chr1:92198258-92198265
5	POLR2A	chr1:92194683-92199275	HepG2	liver:	n/a	n/a
6	BCL3	chr1:92197333-92197701	GM12878	blood:	n/a	chr1:92197586-92197595
7	RELA	chr1:92196977-92198384	GM19193	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
8	EBF1	chr1:92197300-92197685	GM12878	blood:	n/a	n/a
9	STAT3	chr1:92197412-92198356	MCF10A-Er-Src	breast:	n/a	chr1:92198106-92198126 chr1:92197569-92197580 chr1:92198112-92198120 chr1:92198106-92198126 chr1:92198109-92198123 chr1:92197619-92197631 chr1:92198242-92198251
10	TBL1XR1	chr1:92196931-92198817	K562	blood:	n/a	n/a
11	MYC	chr1:92196326-92197851	MCF10A-Er-Src	breast:	n/a	n/a
12	RELA	chr1:92197393-92197727	GM15510	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
13	EBF1	chr1:92197366-92197733	GM12878	blood:	n/a	n/a
14	RELA	chr1:92196892-92198345	GM12891	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
15	EBF1	chr1:92197110-92197776	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:92197555-92198822	K562	blood:	n/a	n/a
17	FOS	chr1:92196969-92197777	MCF10A-Er-Src	breast:	n/a	chr1:92197036-92197047 chr1:92197511-92197520
18	SMARCC1	chr1:92197492-92198470	Hela-S3	cervix:	n/a	chr1:92198242-92198251
19	NR2F2	chr1:92197666-92198962	K562	blood:	n/a	n/a
20	NFIC	chr1:92197358-92197714	SK-N-SH	brain:	n/a	n/a
21	NFIC	chr1:92196917-92198752	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr1:92197322-92198509	MCF10A-Er-Src	breast:	n/a	n/a
23	EP300	chr1:92197216-92198632	ECC-1	luminal epithelium:	n/a	chr1:92198243-92198252
24	FOS	chr1:92196995-92197848	MCF10A-Er-Src	breast:	n/a	chr1:92197036-92197047 chr1:92197511-92197520
25	TCF12	chr1:92196805-92198645	ECC-1	luminal epithelium:	n/a	chr1:92197536-92197544
26	MYC	chr1:92196964-92197792	MCF10A-Er-Src	breast:	n/a	n/a
27	JUN	chr1:92195766-92199113	K562	blood:	n/a	chr1:92197036-92197047 chr1:92198242-92198252 chr1:92198242-92198252 chr1:92197511-92197520 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
28	RELA	chr1:92197366-92197759	GM19099	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
29	IRF1	chr1:92196982-92198812	K562	blood:	n/a	chr1:92197568-92197581 chr1:92198273-92198280 chr1:92198116-92198125 chr1:92198243-92198252 chr1:92197567-92197587 chr1:92197567-92197581
30	EP300	chr1:92196888-92198706	ECC-1	luminal epithelium:	n/a	chr1:92198243-92198252
31	RELA	chr1:92197178-92197789	GM10847	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
32	RAD21	chr1:92197178-92198634	ECC-1	luminal epithelium:	n/a	n/a
33	TEAD4	chr1:92196976-92197880	ECC-1	luminal epithelium:	n/a	n/a
34	FOXM1	chr1:92197105-92198719	ECC-1	luminal epithelium:	n/a	n/a
35	MXI1	chr1:92197568-92198592	IMR90	lung:	n/a	n/a
36	STAT3	chr1:92197345-92197772	MCF10A-Er-Src	breast:	n/a	chr1:92197569-92197580 chr1:92197619-92197631
37	STAT3	chr1:92197449-92197753	MCF10A-Er-Src	breast:	n/a	chr1:92197569-92197580 chr1:92197619-92197631
38	NFIC	chr1:92197031-92198629	ECC-1	luminal epithelium:	n/a	n/a
39	FOS	chr1:92196987-92197726	MCF10A-Er-Src	breast:	n/a	chr1:92197036-92197047 chr1:92197511-92197520
40	BCL3	chr1:92197434-92197789	A549	lung:	n/a	chr1:92197586-92197595
41	RUNX3	chr1:92196829-92198380	GM12878	blood:	n/a	chr1:92197576-92197585 chr1:92197576-92197585
42	IKZF1	chr1:92197348-92198396	GM12878	blood:	n/a	n/a
43	BACH1	chr1:92197491-92198200	K562	blood:	n/a	n/a
44	NFIC	chr1:92196844-92197778	GM12878	blood:	n/a	n/a
45	TCF7L2	chr1:92197480-92198488	Hela-S3	cervix:	n/a	chr1:92198242-92198251
46	MTA3	chr1:92197285-92198387	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:92197364-92197679	U87	brain:	n/a	n/a
48	STAT3	chr1:92197392-92198293	MCF10A-Er-Src	breast:	n/a	chr1:92198106-92198126 chr1:92197569-92197580 chr1:92198112-92198120 chr1:92198106-92198126 chr1:92198109-92198123 chr1:92197619-92197631 chr1:92198242-92198251
49	RELA	chr1:92197000-92198363	GM18505	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
50	BHLHE40	chr1:92196306-92198601	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:92192178..92194320-chr1:92196821..92198679,2	K562	blood:
2	chr1:92195746..92200158-chr1:92212228..92214643,4	K562	blood:
3	chr1:92196121..92198991-chr1:92207192..92209304,2	MCF-7	breast:
4	chr1:92196960..92199922-chr1:92201744..92205146,4	K562	blood:
5	chr1:92186351..92189237-chr1:92195630..92198229,2	K562	blood:
6	chr1:92181357..92183863-chr1:92196120..92197770,2	K562	blood:
7	chr1:92196725..92200248-chr1:92206849..92210560,4	K562	blood:
8	chr1:92197642..92200532-chr1:92350997..92352784,2	K562	blood:
9	chr1:92196718..92198594-chr1:92235219..92237131,2	K562	blood:
10	chr1:92194536..92198402-chr1:92243329..92245903,3	K562	blood:
11	chr1:92197202..92203288-chr1:92206365..92210533,5	K562	blood:
12	chr1:92162441..92164446-chr1:92195933..92198118,2	K562	blood:

Variant related genes	Relation type
TGFBR3	TF binding region
ENSG00000069702	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10783003	0.81[ASN][1000 genomes]
rs10783004	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165354	0.80[ASN][1000 genomes]
rs11165372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165376	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165380	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12069138	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12069176	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12074859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124904	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12403389	0.85[JPT][hapmap]
rs2306886	1.00[CHB][hapmap]
rs2306887	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4658264	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6604051	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512284	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517044	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh 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	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv528991	chr1:92191534-92198162	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92173200-92202400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:92173600-92197800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:92189200-92202200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:92190600-92201400	Genic enhancers	NHDF-Ad	bronchial
5	chr1:92191400-92198400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:92191800-92204000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:92192600-92200600	Genic enhancers	Fetal Muscle Leg	muscle
8	chr1:92193000-92202400	Weak transcription	Aorta	Aorta
9	chr1:92193600-92200600	Strong transcription	HepG2	liver
10	chr1:92194400-92201000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:92194600-92198800	Genic enhancers	Fetal Lung	lung
12	chr1:92195000-92199400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:92195000-92199400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:92195200-92197800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:92195200-92198200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:92195200-92198400	Enhancers	Right Ventricle	heart
17	chr1:92195400-92198000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:92195400-92198400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr1:92195400-92198600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr1:92195400-92198800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr1:92195600-92198000	Enhancers	Primary T cells from cord blood	blood
22	chr1:92195600-92198400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:92195600-92198600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:92195600-92199200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:92195600-92199200	Enhancers	Fetal Thymus	thymus
26	chr1:92195800-92199400	Genic enhancers	Fetal Stomach	stomach
27	chr1:92196000-92198000	Enhancers	Adipose Nuclei	Adipose
28	chr1:92196000-92201200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:92196200-92198000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:92196200-92198200	Enhancers	Liver	Liver
31	chr1:92196200-92198200	Enhancers	Fetal Heart	heart
32	chr1:92196200-92198400	Enhancers	HSMM	muscle
33	chr1:92196200-92198400	Enhancers	NHEK	skin
34	chr1:92196200-92198800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr1:92196200-92198800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr1:92196200-92199000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:92196200-92199000	Enhancers	Colon Smooth Muscle	Colon
38	chr1:92196200-92199200	Genic enhancers	NHLF	lung
39	chr1:92196400-92197800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:92196400-92198000	Genic enhancers	Placenta	Placenta
41	chr1:92196400-92198000	Enhancers	Spleen	Spleen
42	chr1:92196400-92198200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:92196400-92198200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:92196400-92198400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:92196400-92198400	Enhancers	Left Ventricle	heart
46	chr1:92196400-92198400	Enhancers	Right Atrium	heart
47	chr1:92196400-92198400	Enhancers	HMEC	breast
48	chr1:92196400-92198600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:92196400-92198600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr1:92196400-92198800	Enhancers	NH-A	brain

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