Variant report

Variant	rs74089028
Chromosome Location	chr12:49736994-49736995
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	CTBP2	chr12:49735158-49737394	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr12:49736312-49737428	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr12:49736759-49737518	K562	blood:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
4	NR2F2	chr12:49736039-49737343	K562	blood:	n/a	n/a
5	TCF12	chr12:49735929-49737052	A549	lung:	n/a	n/a
6	UBTF	chr12:49736941-49737078	K562	blood:	n/a	n/a
7	SMC3	chr12:49735764-49737092	SK-N-SH	brain:	n/a	chr12:49736375-49736385 chr12:49736209-49736219 chr12:49736484-49736498 chr12:49736484-49736494 chr12:49736375-49736389
8	CTCF	chr12:49736940-49737090	WERI-Rb-1	eye:	n/a	n/a
9	NFIC	chr12:49736096-49737081	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr12:49736162-49737386	A549	lung:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
11	BHLHE40	chr12:49736173-49737372	K562	blood:	n/a	n/a
12	CTCF	chr12:49736860-49737010	GM12872	blood:	n/a	chr12:49736885-49736898
13	RAD21	chr12:49736062-49737090	SK-N-SH	brain:	n/a	chr12:49736789-49736799 chr12:49736374-49736387 chr12:49736375-49736389 chr12:49736884-49736898 chr12:49736375-49736385 chr12:49736371-49736390
14	PBX3	chr12:49735972-49737011	SK-N-SH	brain:	n/a	n/a
15	E2F6	chr12:49736239-49737079	A549	lung:	n/a	chr12:49736641-49736648
16	ZBTB7A	chr12:49735808-49737533	ECC-1	luminal epithelium:	n/a	chr12:49736374-49736383 chr12:49736793-49736801
17	MAX	chr12:49736017-49737563	ECC-1	luminal epithelium:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
18	CTCF	chr12:49735821-49737540	A549	lung:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736885-49736898 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
19	ZBTB7A	chr12:49735973-49737145	ECC-1	luminal epithelium:	n/a	chr12:49736374-49736383 chr12:49736793-49736801
20	MAX	chr12:49735989-49737509	A549	lung:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
21	KAP1	chr12:49736041-49737458	U2OS	brain:	n/a	n/a
22	HDAC2	chr12:49736934-49737421	K562	blood:	n/a	n/a
23	RCOR1	chr12:49736973-49737350	K562	blood:	n/a	n/a
24	CTCF	chr12:49736980-49737130	GM12864	blood:	n/a	n/a
25	CTCF	chr12:49736070-49737003	GM12892	blood:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736885-49736898 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
26	KAP1	chr12:49735830-49737382	HEK293	kidney:	n/a	n/a
27	PBX3	chr12:49735911-49737424	SK-N-SH	brain:	n/a	n/a
28	NR2F2	chr12:49736942-49737316	K562	blood:	n/a	n/a
29	BACH1	chr12:49736346-49737145	H1-hESC	embryonic stem cell:	n/a	n/a
30	BCL3	chr12:49736967-49737381	GM12878	blood:	n/a	n/a
31	TCF12	chr12:49735879-49737500	ECC-1	luminal epithelium:	n/a	chr12:49737328-49737335
32	SIN3A	chr12:49735631-49737614	H1-hESC	embryonic stem cell:	n/a	chr12:49737000-49737013 chr12:49737455-49737463 chr12:49735808-49735821

No.	Distal block	Cell Line	Cell type
1	chr12:49734512..49737434-chr12:49761201..49764804,3	K562	blood:
2	chr12:49656587..49660636-chr12:49733539..49743833,13	K562	blood:
3	chr12:49709675..49711213-chr12:49736436..49739309,2	MCF-7	breast:
4	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
5	chr12:49681835..49682776-chr12:49735729..49737096,6	MCF-7	breast:
6	chr12:49668999..49670991-chr12:49736933..49738497,2	K562	blood:
7	chr12:49725155..49726080-chr12:49735903..49737150,6	MCF-7	breast:
8	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
9	chr12:49725123..49726098-chr12:49735996..49737262,7	K562	blood:
10	chr12:49685452..49688091-chr12:49734714..49737225,2	MCF-7	breast:
11	chr12:49662709..49665978-chr12:49735321..49738677,4	K562	blood:
12	chr12:49735114..49738057-chr12:49759505..49762701,3	K562	blood:
13	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
14	chr12:49661766..49665978-chr12:49735321..49738677,5	K562	blood:

Variant related genes	Relation type
DNAJC22	TF binding region
ENSG00000123352	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000135406	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11830820	1.00[AMR][1000 genomes]
rs11836976	1.00[AMR][1000 genomes]
rs17853062	1.00[AMR][1000 genomes]
rs56005192	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56014465	1.00[AMR][1000 genomes]
rs56140046	1.00[AMR][1000 genomes]
rs56330550	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57546911	1.00[AMR][1000 genomes]
rs58557116	1.00[AMR][1000 genomes]
rs59493874	1.00[AMR][1000 genomes]
rs60712360	1.00[AMR][1000 genomes]
rs60865902	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61110708	1.00[AMR][1000 genomes]
rs7296117	1.00[AMR][1000 genomes]
rs7299056	1.00[AMR][1000 genomes]
rs7309243	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089008	1.00[AMR][1000 genomes]
rs74089010	1.00[AMR][1000 genomes]
rs74089030	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089561	1.00[AMR][1000 genomes]
rs74089565	1.00[AMR][1000 genomes]
rs74091029	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49734200-49739400	Weak transcription	Hela-S3	cervix
2	chr12:49735000-49737000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:49735400-49737000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr12:49735400-49737000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:49735400-49737200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:49735600-49737000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr12:49735600-49737000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:49735600-49737400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:49735800-49737000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr12:49735800-49737000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
11	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
13	chr12:49735800-49737200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
16	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
17	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
19	chr12:49735800-49737800	Enhancers	Gastric	stomach
20	chr12:49736000-49737000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:49736000-49737000	Active TSS	A549	lung
22	chr12:49736000-49737000	Bivalent/Poised TSS	HSMM	muscle
23	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
24	chr12:49736000-49737200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	NH-A	brain
29	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:49736000-49737400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
33	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
35	chr12:49736000-49737400	Enhancers	Lung	lung
36	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
37	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
38	chr12:49736000-49737600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
39	chr12:49736000-49737800	Enhancers	Pancreas	Pancrea
40	chr12:49736200-49737000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
41	chr12:49736200-49737000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr12:49736200-49737000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
43	chr12:49736200-49737000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
44	chr12:49736200-49737000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr12:49736200-49737000	Flanking Active TSS	Ovary	ovary
46	chr12:49736200-49737000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr12:49736200-49737000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
48	chr12:49736200-49737000	Flanking Bivalent TSS/Enh	NHLF	lung
49	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
50	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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