Variant report

Variant	rs12070846
Chromosome Location	chr1:92197098-92197099
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	EGR1	chr1:92196908-92197269	K562	blood:	n/a	chr1:92197130-92197152
2	POLR2A	chr1:92196755-92197288	K562	blood:	n/a	n/a
3	TCF3	chr1:92197015-92197209	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:92194683-92199275	HepG2	liver:	n/a	n/a
5	RAD21	chr1:92196921-92197142	K562	blood:	n/a	n/a
6	MAZ	chr1:92196801-92197240	K562	blood:	n/a	n/a
7	RELA	chr1:92196977-92198384	GM19193	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
8	TBP	chr1:92196908-92197184	K562	blood:	n/a	n/a
9	TEAD4	chr1:92196776-92197264	K562	blood:	n/a	n/a
10	RCOR1	chr1:92196293-92197280	K562	blood:	n/a	n/a
11	NR2F2	chr1:92196744-92197534	K562	blood:	n/a	n/a
12	FOS	chr1:92196985-92197126	MCF10A-Er-Src	breast:	n/a	chr1:92197036-92197047
13	TBL1XR1	chr1:92196931-92198817	K562	blood:	n/a	n/a
14	MYC	chr1:92196326-92197851	MCF10A-Er-Src	breast:	n/a	n/a
15	CUX1	chr1:92196918-92197110	K562	blood:	n/a	n/a
16	POLR2A	chr1:92196825-92197544	PFSK-1	brain:	n/a	n/a
17	RELA	chr1:92196892-92198345	GM12891	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
18	TBL1XR1	chr1:92196865-92197266	K562	blood:	n/a	n/a
19	MAFK	chr1:92196935-92197170	K562	blood:	n/a	n/a
20	FOS	chr1:92196969-92197777	MCF10A-Er-Src	breast:	n/a	chr1:92197036-92197047 chr1:92197511-92197520
21	STAT5A	chr1:92196848-92197332	K562	blood:	n/a	n/a
22	MAX	chr1:92196341-92197132	K562	blood:	n/a	n/a
23	EGR1	chr1:92196896-92197295	K562	blood:	n/a	chr1:92197130-92197152
24	POLR2A	chr1:92196816-92197412	PFSK-1	brain:	n/a	n/a
25	CHD2	chr1:92196763-92197187	K562	blood:	n/a	n/a
26	NFIC	chr1:92196917-92198752	ECC-1	luminal epithelium:	n/a	n/a
27	EP300	chr1:92196334-92197283	K562	blood:	n/a	n/a
28	FOS	chr1:92196995-92197848	MCF10A-Er-Src	breast:	n/a	chr1:92197036-92197047 chr1:92197511-92197520
29	YY1	chr1:92196910-92197224	K562	blood:	n/a	n/a
30	TCF12	chr1:92196805-92198645	ECC-1	luminal epithelium:	n/a	chr1:92197536-92197544
31	MYC	chr1:92196964-92197792	MCF10A-Er-Src	breast:	n/a	n/a
32	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
33	MXI1	chr1:92196970-92197115	K562	blood:	n/a	n/a
34	ZMIZ1	chr1:92196746-92197287	K562	blood:	n/a	n/a
35	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
36	EP300	chr1:92196888-92198706	ECC-1	luminal epithelium:	n/a	chr1:92198243-92198252
37	TEAD4	chr1:92196976-92197880	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr1:92197017-92197117	K562	blood:	n/a	n/a
39	YY1	chr1:92196885-92197132	K562	blood:	n/a	n/a
40	MAX	chr1:92196776-92197302	K562	blood:	n/a	n/a
41	POLR2A	chr1:92196796-92197178	K562	blood:	n/a	n/a
42	POLR2A	chr1:92196819-92197222	K562	blood:	n/a	n/a
43	RCOR1	chr1:92196936-92197316	K562	blood:	n/a	n/a
44	UBTF	chr1:92196846-92197211	K562	blood:	n/a	n/a
45	HDAC2	chr1:92196870-92197253	K562	blood:	n/a	n/a
46	NFIC	chr1:92197031-92198629	ECC-1	luminal epithelium:	n/a	n/a
47	FOS	chr1:92196987-92197726	MCF10A-Er-Src	breast:	n/a	chr1:92197036-92197047 chr1:92197511-92197520
48	MAX	chr1:92196906-92197228	K562	blood:	n/a	n/a
49	RUNX3	chr1:92196887-92197249	GM12878	blood:	n/a	n/a
50	RUNX3	chr1:92196829-92198380	GM12878	blood:	n/a	chr1:92197576-92197585 chr1:92197576-92197585

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	chr1:92177009..92179682-chr1:92195748..92197642,2	K562	blood:
6	chr1:92186351..92189237-chr1:92195630..92198229,2	K562	blood:
7	chr1:92181357..92183863-chr1:92196120..92197770,2	K562	blood:
8	chr1:92196725..92200248-chr1:92206849..92210560,4	K562	blood:
9	chr1:92196718..92198594-chr1:92235219..92237131,2	K562	blood:
10	chr1:92194536..92198402-chr1:92243329..92245903,3	K562	blood:
11	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: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11165300	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11165377	0.83[AMR][1000 genomes]
rs17512269	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2046736	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6662887	0.84[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	chr1:92185800-92197600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:92189200-92202200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:92190600-92201400	Genic enhancers	NHDF-Ad	bronchial
6	chr1:92191400-92198400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:92191800-92204000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:92192600-92197600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:92192600-92200600	Genic enhancers	Fetal Muscle Leg	muscle
10	chr1:92193000-92202400	Weak transcription	Aorta	Aorta
11	chr1:92193600-92200600	Strong transcription	HepG2	liver
12	chr1:92194400-92201000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:92194600-92198800	Genic enhancers	Fetal Lung	lung
14	chr1:92195000-92197200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:92195000-92199400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:92195000-92199400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:92195200-92197200	Enhancers	GM12878-XiMat	blood
18	chr1:92195200-92197800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:92195200-92198200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:92195200-92198400	Enhancers	Right Ventricle	heart
21	chr1:92195400-92198000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:92195400-92198400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:92195400-92198600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:92195400-92198800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:92195600-92197200	Weak transcription	Fetal Kidney	kidney
26	chr1:92195600-92197600	Enhancers	Hela-S3	cervix
27	chr1:92195600-92198000	Enhancers	Primary T cells from cord blood	blood
28	chr1:92195600-92198400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:92195600-92198600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:92195600-92199200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:92195600-92199200	Enhancers	Fetal Thymus	thymus
32	chr1:92195800-92197200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:92195800-92197600	Weak transcription	Fetal Intestine Large	intestine
34	chr1:92195800-92199400	Genic enhancers	Fetal Stomach	stomach
35	chr1:92196000-92197200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:92196000-92198000	Enhancers	Adipose Nuclei	Adipose
37	chr1:92196000-92201200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr1:92196200-92198000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:92196200-92198200	Enhancers	Liver	Liver
40	chr1:92196200-92198200	Enhancers	Fetal Heart	heart
41	chr1:92196200-92198400	Enhancers	HSMM	muscle
42	chr1:92196200-92198400	Enhancers	NHEK	skin
43	chr1:92196200-92198800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:92196200-92198800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr1:92196200-92199000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:92196200-92199000	Enhancers	Colon Smooth Muscle	Colon
47	chr1:92196200-92199200	Genic enhancers	NHLF	lung
48	chr1:92196400-92197200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr1:92196400-92197400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:92196400-92197800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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