Variant report

Variant	rs12448829
Chromosome Location	chr16:75497340-75497341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75497233-75498857	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr16:75497302-75497471	MCF-7	breast:	n/a	n/a
3	CTCF	chr16:75497287-75497481	MCF-7	breast:	n/a	n/a
4	POLR2A	chr16:75497193-75498959	K562	blood:	n/a	n/a
5	POLR2A	chr16:75496990-75498909	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:75497307-75497850	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr16:75497335-75497432	LNCaP	prostate:	n/a	n/a
8	TAF1	chr16:75497236-75498916	HepG2	liver:	n/a	n/a
9	POLR2A	chr16:75497162-75497564	GM12878	blood:	n/a	n/a
10	CTCF	chr16:75497260-75497410	HMEC	breast:	n/a	n/a
11	POLR2A	chr16:75497085-75497708	GM12878	blood:	n/a	n/a
12	POLR2A	chr16:75497318-75497578	GM12878	blood:	n/a	n/a
13	EBF1	chr16:75497131-75497525	GM12878	blood:	n/a	n/a
14	POLR2A	chr16:75497220-75497924	Hela-S3	cervix:	n/a	n/a
15	MYC	chr16:75497275-75497477	HepG2	liver:	n/a	n/a
16	RUNX3	chr16:75496728-75497404	GM12878	blood:	n/a	n/a
17	POLR2A	chr16:75497228-75497755	HepG2	liver:	n/a	n/a
18	CTCF	chr16:75497293-75497466	MCF-7	breast:	n/a	n/a
19	HEY1	chr16:75497122-75498873	HepG2	liver:	n/a	chr16:75497902-75497917 chr16:75498319-75498334
20	POLR2A	chr16:75497024-75498978	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr16:75497152-75498894	MCF-7	breast:	n/a	n/a
22	POLR2A	chr16:75497187-75497576	GM12892	blood:	n/a	n/a
23	POLR2A	chr16:75497198-75498821	GM12878	blood:	n/a	n/a
24	SIN3AK20	chr16:75497205-75497567	HepG2	liver:	n/a	n/a
25	TCF12	chr16:75497188-75497404	GM12878	blood:	n/a	chr16:75497373-75497380
26	CTCF	chr16:75497336-75497455	MCF-7	breast:	n/a	n/a
27	MYC	chr16:75497294-75497412	MCF-7	breast:	n/a	n/a
28	POLR2A	chr16:75497187-75498025	HepG2	liver:	n/a	n/a
29	POLR2A	chr16:75497194-75497485	HepG2	liver:	n/a	n/a
30	POLR2A	chr16:75497286-75497590	MCF-7	breast:	n/a	n/a
31	TAF1	chr16:75497263-75498892	H1-hESC	embryonic stem cell:	n/a	n/a
32	MYBL2	chr16:75497167-75499127	HepG2	liver:	n/a	n/a
33	POLR2A	chr16:75497261-75498924	MCF-7	breast:	n/a	n/a
34	CTCF	chr16:75497260-75497410	HAc	cerebellar:	n/a	n/a
35	CTCF	chr16:75497280-75497430	HMEC	breast:	n/a	n/a
36	POLR2A	chr16:75497204-75497829	HepG2	liver:	n/a	n/a
37	BATF	chr16:75497068-75497480	GM12878	blood:	n/a	n/a
38	CTCF	chr16:75497291-75497476	MCF-7	breast:	n/a	n/a
39	POLR2A	chr16:75497300-75497552	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr16:75497275-75497548	GM12878	blood:	n/a	n/a
41	JUND	chr16:75497178-75497732	HepG2	liver:	n/a	n/a
42	POLR2A	chr16:75497126-75497587	ProgFib	skin:	n/a	n/a
43	POLR2A	chr16:75497334-75497573	Hela-S3	cervix:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75497125..75499382-chr16:75564750..75566395,2	MCF-7	breast:
2	chr16:75495533..75500726-chr16:75509549..75515784,9	MCF-7	breast:
3	chr16:75465991..75469604-chr16:75494524..75499996,12	MCF-7	breast:
4	chr16:75497166..75499836-chr16:75598619..75601609,5	MCF-7	breast:
5	chr16:75496396..75498894-chr16:75652662..75656672,3	MCF-7	breast:
6	chr16:75492503..75494041-chr16:75496484..75498203,2	K562	blood:
7	chr16:75475154..75477431-chr16:75495274..75497923,2	MCF-7	breast:
8	chr16:75492483..75495341-chr16:75495841..75499470,4	K562	blood:
9	chr16:75495991..75500241-chr16:75679416..75683319,6	MCF-7	breast:
10	chr16:75496436..75498553-chr16:75596400..75601675,4	MCF-7	breast:
11	chr16:75496858..75499850-chr16:75589381..75591063,2	K562	blood:
12	chr16:75496672..75499382-chr16:75549463..75551344,4	MCF-7	breast:
13	chr16:75496580..75498737-chr16:75588829..75590831,2	MCF-7	breast:
14	chr16:75497002..75498653-chr16:75549372..75551463,2	K562	blood:
15	chr16:75464062..75469543-chr16:75495268..75500189,14	MCF-7	breast:
16	chr16:75496764..75498931-chr16:75589140..75591199,3	MCF-7	breast:
17	chr16:75181464..75183944-chr16:75497097..75499788,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261476	TF binding region
ENSG00000184517	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000135702	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000034713	Chromatin interaction
ENSG00000203472	Chromatin interaction
ENSG00000262583	Chromatin interaction
ENSG00000261476	Chromatin interaction
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1030261	0.84[ASN][1000 genomes]
rs1030262	0.85[ASN][1000 genomes]
rs10871312	0.84[ASN][1000 genomes]
rs10871313	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11149831	0.81[AMR][1000 genomes]
rs11641249	0.83[ASN][1000 genomes]
rs11641430	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11643207	0.87[ASN][1000 genomes]
rs11644306	0.84[ASN][1000 genomes]
rs11649638	0.84[ASN][1000 genomes]
rs12051137	0.85[ASN][1000 genomes]
rs12446877	0.84[ASN][1000 genomes]
rs12918797	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12924333	0.82[ASN][1000 genomes]
rs12927562	0.83[ASN][1000 genomes]
rs12928036	0.83[ASN][1000 genomes]
rs12933281	0.83[ASN][1000 genomes]
rs1424013	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17696831	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1834013	0.87[ASN][1000 genomes]
rs1834014	0.87[ASN][1000 genomes]
rs2161684	0.82[ASN][1000 genomes]
rs28558946	0.84[ASN][1000 genomes]
rs28655617	0.82[ASN][1000 genomes]
rs3115960	0.80[ASN][1000 genomes]
rs34539062	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34918083	0.87[ASN][1000 genomes]
rs34996006	0.80[ASN][1000 genomes]
rs35214308	0.80[ASN][1000 genomes]
rs35683383	0.82[ASN][1000 genomes]
rs37592	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37593	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37594	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37595	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37597	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs37606	0.83[ASN][1000 genomes]
rs40446	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887829	0.84[ASN][1000 genomes]
rs4888425	0.80[ASN][1000 genomes]
rs4888426	0.80[ASN][1000 genomes]
rs4888427	0.82[ASN][1000 genomes]
rs4888430	0.87[ASN][1000 genomes]
rs4888431	0.85[ASN][1000 genomes]
rs56116092	0.81[ASN][1000 genomes]
rs59155720	0.82[ASN][1000 genomes]
rs59465235	0.83[ASN][1000 genomes]
rs62060550	0.87[ASN][1000 genomes]
rs62060551	0.87[ASN][1000 genomes]
rs6564261	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7193828	0.80[ASN][1000 genomes]
rs7194035	0.80[ASN][1000 genomes]
rs7195161	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7199062	0.80[ASN][1000 genomes]
rs7200053	0.80[ASN][1000 genomes]
rs7202596	0.84[ASN][1000 genomes]
rs7204984	0.80[ASN][1000 genomes]
rs7206665	0.80[ASN][1000 genomes]
rs8055490	0.83[ASN][1000 genomes]
rs8056141	0.87[ASN][1000 genomes]
rs8057084	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8063068	0.83[ASN][1000 genomes]
rs977985	0.86[ASN][1000 genomes]
rs977987	0.86[ASN][1000 genomes]
rs9933255	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[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	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
10	esv3437619	chr16:75496876-75499424	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12448829	RP11-252K23.2	cis	lung	GTEx
rs12448829	RP11-252K23.2	cis	Nerve Tibial	GTEx
rs12448829	RP11-252K23.2	cis	Thyroid	GTEx
rs12448829	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs12448829	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs12448829	RP11-252K23.2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75469400-75497400	Weak transcription	Psoas Muscle	Psoas
2	chr16:75481800-75497600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:75485800-75497400	Weak transcription	Fetal Brain Female	brain
4	chr16:75485800-75497600	Weak transcription	Aorta	Aorta
5	chr16:75489800-75497400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr16:75491800-75497400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr16:75492600-75497400	Weak transcription	Pancreas	Pancrea
8	chr16:75493000-75497400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr16:75494000-75497400	Weak transcription	Gastric	stomach
10	chr16:75494400-75497400	Enhancers	Fetal Lung	lung
11	chr16:75494600-75497400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr16:75494600-75497400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:75494600-75497400	Weak transcription	Left Ventricle	heart
14	chr16:75494800-75497600	Weak transcription	Ovary	ovary
15	chr16:75495200-75497600	Weak transcription	Lung	lung
16	chr16:75495400-75497400	Weak transcription	Small Intestine	intestine
17	chr16:75495800-75497400	Active TSS	Fetal Brain Male	brain
18	chr16:75496000-75497400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr16:75496000-75497600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr16:75496000-75499000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr16:75496400-75497400	Enhancers	Primary B cells from peripheral blood	blood
22	chr16:75496400-75497600	Enhancers	Primary B cells from cord blood	blood
23	chr16:75496600-75497400	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr16:75496600-75497400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr16:75496600-75497800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr16:75496600-75497800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:75496600-75497800	Flanking Active TSS	Dnd41	blood
28	chr16:75496600-75498000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr16:75496600-75498800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr16:75496600-75498800	Active TSS	GM12878-XiMat	blood
31	chr16:75496600-75499000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr16:75496800-75497400	Enhancers	Brain Angular Gyrus	brain
33	chr16:75496800-75497400	Enhancers	Thymus	Thymus
34	chr16:75496800-75497600	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr16:75496800-75498000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr16:75496800-75498000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr16:75496800-75498800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr16:75497000-75497400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr16:75497000-75497400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr16:75497000-75497400	Flanking Active TSS	Fetal Stomach	stomach
41	chr16:75497000-75497400	Enhancers	Fetal Thymus	thymus
42	chr16:75497000-75497400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr16:75497000-75497400	Enhancers	HSMMtube	muscle
44	chr16:75497000-75497400	Enhancers	NH-A	brain
45	chr16:75497000-75497600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr16:75497000-75497600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr16:75497000-75497600	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr16:75497000-75497600	Weak transcription	Stomach Mucosa	stomach
49	chr16:75497000-75497600	Flanking Active TSS	HUVEC	blood vessel
50	chr16:75497000-75497600	Flanking Active TSS	Osteobl	bone

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