Variant report

Variant	rs60865902
Chromosome Location	chr12:49741388-49741389
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	CTCF	chr12:49741360-49741737	T-47D	breast:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569
2	PAX5	chr12:49740952-49741728	GM12878	blood:	n/a	chr12:49741295-49741313 chr12:49741297-49741314 chr12:49741296-49741315
3	MAX	chr12:49740402-49742031	MCF-7	breast:	n/a	n/a
4	CTCF	chr12:49741340-49741490	RPTEC	kidney:	n/a	n/a
5	CTCF	chr12:49741196-49741705	GM19239	blood:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569
6	YY1	chr12:49741340-49741732	GM12892	blood:	n/a	chr12:49741710-49741721 chr12:49741662-49741676 chr12:49741565-49741577 chr12:49741552-49741566
7	GTF2F1	chr12:49740854-49741837	Hela-S3	cervix:	n/a	n/a
8	MAX	chr12:49740385-49742027	ECC-1	luminal epithelium:	n/a	n/a
9	EGR1	chr12:49741199-49741709	K562	blood:	n/a	n/a
10	CTCF	chr12:49741380-49741530	HA-sp	spinal cord:	n/a	n/a
11	TCF12	chr12:49740213-49742052	ECC-1	luminal epithelium:	n/a	chr12:49741032-49741042
12	CTCF	chr12:49741350-49741756	K562	blood:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569
13	CTCF	chr12:49741360-49741510	NHDF-neo	bronchial:	n/a	n/a
14	KAP1	chr12:49740630-49741894	HEK293	kidney:	n/a	n/a
15	SP1	chr12:49741262-49742139	A549	lung:	n/a	chr12:49741868-49741882
16	RAD21	chr12:49741222-49741896	MCF-7	breast:	n/a	chr12:49741554-49741566 chr12:49741552-49741571 chr12:49741556-49741570 chr12:49741706-49741716
17	USF2	chr12:49741330-49741617	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOSL2	chr12:49740940-49742510	A549	lung:	n/a	chr12:49742311-49742320 chr12:49741845-49741854 chr12:49742312-49742319 chr12:49742311-49742319 chr12:49741670-49741679 chr12:49742307-49742318
19	CTCF	chr12:49741360-49741510	NHLF	lung:	n/a	n/a
20	MAX	chr12:49740435-49742080	A549	lung:	n/a	n/a
21	E2F6	chr12:49740549-49741539	K562	blood:	n/a	chr12:49740739-49740750 chr12:49740613-49740622
22	JUND	chr12:49741377-49741764	K562	blood:	n/a	chr12:49741670-49741679
23	ZBTB7A	chr12:49738646-49742163	ECC-1	luminal epithelium:	n/a	chr12:49739274-49739281 chr12:49741924-49741935 chr12:49741555-49741564
24	EGR1	chr12:49741176-49741951	HCT-116	colon:	n/a	chr12:49741709-49741719
25	MBD4	chr12:49741344-49741953	HepG2	liver:	n/a	n/a
26	CTCF	chr12:49741360-49741650	A549	lung:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569
27	CTCF	chr12:49740978-49741984	HCT-116	colon:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569
28	MAZ	chr12:49740986-49741872	Hela-S3	cervix:	n/a	n/a
29	YY1	chr12:49741328-49741729	H1-hESC	embryonic stem cell:	n/a	chr12:49741710-49741721 chr12:49741662-49741676 chr12:49741565-49741577 chr12:49741552-49741566
30	ZBTB7A	chr12:49741380-49741740	HepG2	liver:	n/a	chr12:49741555-49741564
31	SP1	chr12:49741156-49742136	A549	lung:	n/a	chr12:49741189-49741202 chr12:49741868-49741882
32	KAP1	chr12:49740560-49741698	U2OS	brain:	n/a	n/a
33	FOXM1	chr12:49741331-49741736	GM12878	blood:	n/a	n/a
34	CTCF	chr12:49741370-49741799	H1-hESC	embryonic stem cell:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569
35	CTCF	chr12:49741371-49741764	A549	lung:	n/a	chr12:49741554-49741572 chr12:49741549-49741570 chr12:49741555-49741571 chr12:49741556-49741569 chr12:49741556-49741569
36	EBF1	chr12:49741360-49741915	GM12878	blood:	n/a	chr12:49741722-49741733 chr12:49741703-49741714
37	TCF12	chr12:49740418-49742001	ECC-1	luminal epithelium:	n/a	chr12:49741032-49741042
38	YY1	chr12:49741344-49742010	HepG2	liver:	n/a	chr12:49741710-49741721 chr12:49741662-49741676 chr12:49741565-49741577 chr12:49741552-49741566
39	HMGN3	chr12:49741372-49741826	K562	blood:	n/a	n/a
40	YY1	chr12:49741362-49741990	A549	lung:	n/a	chr12:49741710-49741721 chr12:49741662-49741676 chr12:49741565-49741577 chr12:49741552-49741566
41	YY1	chr12:49741358-49741809	SK-N-SH_RA	brain:	n/a	chr12:49741710-49741721 chr12:49741662-49741676 chr12:49741565-49741577 chr12:49741552-49741566
42	EP300	chr12:49741306-49742392	A549	lung:	n/a	chr12:49742310-49742319 chr12:49741615-49741631 chr12:49742311-49742320
43	REST	chr12:49741010-49742198	A549	lung:	n/a	chr12:49741422-49741442 chr12:49741591-49741604 chr12:49741582-49741595
44	TAF1	chr12:49741383-49742195	A549	lung:	n/a	n/a
45	PAX5	chr12:49740922-49741744	GM12892	blood:	n/a	chr12:49741295-49741313 chr12:49741297-49741314 chr12:49741296-49741315
46	EP300	chr12:49741370-49741893	T-47D	breast:	n/a	chr12:49741615-49741631
47	TBL1XR1	chr12:49741388-49741685	K562	blood:	n/a	n/a
48	MAZ	chr12:49741206-49741905	HepG2	liver:	n/a	n/a
49	CTCF	chr12:49741360-49741510	HFF-Myc	foreskin:	n/a	n/a
50	RAD21	chr12:49741313-49741759	H1-hESC	embryonic stem cell:	n/a	chr12:49741554-49741566 chr12:49741552-49741571 chr12:49741556-49741570 chr12:49741706-49741716

No.	Distal block	Cell Line	Cell type
1	chr12:49688782..49690788-chr12:49741064..49743191,2	MCF-7	breast:
2	chr12:49739423..49741666-chr12:49907974..49910735,2	MCF-7	breast:
3	chr12:49691871..49692482-chr12:49741193..49741985,2	MCF-7	breast:
4	chr12:49656587..49660636-chr12:49733539..49743833,13	K562	blood:
5	chr12:49741030..49742987-chr12:49986875..49988929,2	K562	blood:
6	chr12:49740832..49741606-chr12:49942595..49943430,2	K562	blood:
7	chr12:49739131..49745064-chr12:49758784..49762517,10	MCF-7	breast:
8	chr12:49683076..49686072-chr12:49740867..49742928,2	MCF-7	breast:
9	chr12:49657182..49662198-chr12:49738070..49742868,13	MCF-7	breast:
10	chr12:49740569..49744952-chr12:49759719..49761508,3	K562	blood:
11	chr12:49726361..49727184-chr12:49741012..49741811,2	K562	blood:
12	chr12:49740075..49745225-chr12:49756992..49761732,8	K562	blood:
13	chr12:49740266..49744152-chr12:49960185..49963713,4	MCF-7	breast:
14	chr12:49715312..49722303-chr12:49739075..49744198,13	MCF-7	breast:
15	chr12:49741114..49742103-chr12:50016468..50017223,2	K562	blood:
16	chr12:49725094..49726383-chr12:49741023..49741965,3	MCF-7	breast:
17	chr12:49681907..49682823-chr12:49741104..49742122,6	MCF-7	breast:
18	chr12:49725108..49725946-chr12:49741085..49742047,4	K562	blood:
19	chr12:49740264..49744957-chr12:49759411..49762039,7	MCF-7	breast:
20	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
21	chr12:49741089..49742059-chr12:49973951..49974946,3	K562	blood:
22	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
23	chr12:49730689..49731576-chr12:49741266..49741832,2	MCF-7	breast:

Variant related genes	Relation type
DNAJC22	TF binding region
ENSG00000135451	Chromatin interaction
ENSG00000199237	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000258284	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000167553	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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56014465	1.00[AMR][1000 genomes]
rs56140046	1.00[AMR][1000 genomes]
rs56330550	0.87[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]
rs61110708	1.00[AMR][1000 genomes]
rs7296117	1.00[AMR][1000 genomes]
rs7299056	1.00[AMR][1000 genomes]
rs7309243	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089008	1.00[AMR][1000 genomes]
rs74089010	1.00[AMR][1000 genomes]
rs74089028	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089030	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089031	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089060	0.90[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	chr12:49738800-49741400	Bivalent Enhancer	Fetal Thymus	thymus
2	chr12:49738800-49741800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr12:49738800-49742000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:49738800-49742000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr12:49738800-49742000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:49739000-49741400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:49739000-49741800	Active TSS	Aorta	Aorta
8	chr12:49739000-49742000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:49739000-49742000	Enhancers	Lung	lung
10	chr12:49739000-49742200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:49739200-49742000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
12	chr12:49739200-49742200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
13	chr12:49739400-49741400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
14	chr12:49739400-49741400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:49739400-49741400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:49739400-49741400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:49739400-49741600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
18	chr12:49739400-49741600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:49739400-49741800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
20	chr12:49739400-49741800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:49739400-49741800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
22	chr12:49739400-49741800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:49739400-49741800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:49739400-49741800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
25	chr12:49739400-49742000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr12:49739400-49742000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr12:49739400-49742000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
28	chr12:49739400-49742000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr12:49739400-49742200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:49739600-49741400	Enhancers	Gastric	stomach
31	chr12:49739600-49742400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
32	chr12:49739800-49741600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:49740000-49741600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:49740000-49741600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
35	chr12:49740200-49741400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:49740200-49741400	Flanking Bivalent TSS/Enh	HMEC	breast
37	chr12:49740200-49741400	Flanking Bivalent TSS/Enh	Osteobl	bone
38	chr12:49740200-49741600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
39	chr12:49740200-49741600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:49740200-49741600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:49740200-49741600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:49740200-49742000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
43	chr12:49740200-49742200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:49740400-49741400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
45	chr12:49740400-49741600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
46	chr12:49740400-49741600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:49740400-49741600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
48	chr12:49740400-49741800	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
49	chr12:49740400-49742000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
50	chr12:49740400-49742000	Enhancers	Spleen	Spleen

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