Variant report

Variant	rs4898546
Chromosome Location	chr12:50478449-50478450
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:50478438-50479186	K562	blood:	n/a	chr12:50478768-50478777
2	CTCF	chr12:50478292-50479283	SK-N-SH	brain:	n/a	chr12:50478890-50478903
3	POLR2A	chr12:50477999-50480078	HepG2	liver:	n/a	n/a
4	BCL3	chr12:50478419-50479168	A549	lung:	n/a	n/a
5	POLR2A	chr12:50478434-50480257	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr12:50478411-50479207	ECC-1	luminal epithelium:	n/a	chr12:50478768-50478777
7	CHD1	chr12:50478135-50479792	IMR90	lung:	n/a	n/a
8	MAX	chr12:50478417-50479469	A549	lung:	n/a	chr12:50478768-50478777
9	MXI1	chr12:50478105-50480000	SK-N-SH	brain:	n/a	n/a
10	REST	chr12:50478417-50479345	A549	lung:	n/a	n/a
11	TEAD4	chr12:50478345-50479485	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr12:50478351-50479543	MCF-7	breast:	n/a	chr12:50478768-50478777
13	SP2	chr12:50478412-50479219	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIX5	chr12:50478263-50479087	A549	lung:	n/a	n/a
15	MYBL2	chr12:50478420-50479094	HepG2	liver:	n/a	n/a
16	CTCF	chr12:50478400-50478550	GM06990	blood:	n/a	n/a
17	CEBPB	chr12:50478415-50479100	GM12878	blood:	n/a	n/a
18	GABPA	chr12:50478357-50479487	MCF-7	breast:	n/a	n/a
19	MAX	chr12:50478432-50479268	ECC-1	luminal epithelium:	n/a	chr12:50478768-50478777
20	NFIC	chr12:50478398-50479106	GM12878	blood:	n/a	n/a
21	FOSL2	chr12:50478325-50479066	A549	lung:	n/a	n/a
22	NR2F2	chr12:50478415-50478998	K562	blood:	n/a	n/a
23	POLR2A	chr12:50478433-50479315	GM12878	blood:	n/a	n/a
24	TEAD4	chr12:50478425-50479090	K562	blood:	n/a	n/a
25	CTCF	chr12:50478420-50478570	NHLF	lung:	n/a	n/a
26	SP1	chr12:50478427-50479442	A549	lung:	n/a	chr12:50478971-50478981 chr12:50478971-50478981
27	HCFC1	chr12:50478275-50480063	Hela-S3	cervix:	n/a	n/a
28	TCF12	chr12:50478379-50479603	A549	lung:	n/a	n/a
29	MXI1	chr12:50478152-50479433	IMR90	lung:	n/a	n/a
30	NFIC	chr12:50478298-50479152	ECC-1	luminal epithelium:	n/a	n/a
31	BCL3	chr12:50478436-50479123	A549	lung:	n/a	n/a
32	MTA3	chr12:50478397-50479798	GM12878	blood:	n/a	n/a
33	NR2F2	chr12:50478394-50479346	MCF-7	breast:	n/a	n/a
34	SIN3AK20	chr12:50478398-50479019	A549	lung:	n/a	n/a
35	SIN3AK20	chr12:50478427-50479574	MCF-7	breast:	n/a	n/a
36	REST	chr12:50478417-50480009	H1-neurons	neurons:	n/a	n/a
37	MAX	chr12:50478396-50479594	A549	lung:	n/a	chr12:50478768-50478777
38	GABPA	chr12:50478436-50479443	A549	lung:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50476634..50479276-chr12:50493202..50495258,2	K562	blood:
2	chr12:50477150..50481052-chr12:50559881..50562931,6	MCF-7	breast:
3	chr12:50477499..50479020-chr12:50528748..50530881,2	MCF-7	breast:
4	chr12:50477720..50479464-chr12:50594213..50596665,2	MCF-7	breast:
5	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
6	chr12:50279366..50281726-chr12:50476723..50478563,2	MCF-7	breast:
7	chr12:50472028..50474859-chr12:50477717..50480636,3	MCF-7	breast:
8	chr12:50477580..50479686-chr17:62501151..62502654,2	MCF-7	breast:
9	chr12:50478149..50480392-chr17:58677532..58679268,2	MCF-7	breast:
10	chr12:50477670..50481382-chr12:50495555..50500836,7	K562	blood:
11	chr12:50478449..50481902-chr12:50536030..50539935,3	MCF-7	breast:
12	chr12:50475132..50479699-chr12:50479828..50484275,5	K562	blood:
13	chr12:50477885..50480264-chr12:50559751..50562542,2	K562	blood:
14	chr12:50477576..50479559-chr12:50526628..50528314,2	MCF-7	breast:
15	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
16	chr12:50469904..50470842-chr12:50478448..50479302,2	K562	blood:
17	chr12:50477100..50479136-chr12:50582674..50585443,2	K562	blood:
18	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
19	chr12:50461826..50464798-chr12:50477927..50479451,2	K562	blood:
20	chr12:50477688..50480373-chr12:50497434..50499573,3	K562	blood:
21	chr12:50477178..50480105-chr12:50648113..50650406,2	K562	blood:
22	chr12:50235441..50237993-chr12:50478392..50480338,2	K562	blood:
23	chr12:50464456..50466840-chr12:50477683..50480596,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMARCD1	TF binding region
ENSG00000178449	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000212496	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000257298	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000170836	Chromatin interaction
ENSG00000272368	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10875995	0.96[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs10875996	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169270	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs11169282	0.84[GIH][hapmap]
rs1554844	0.84[GIH][hapmap]
rs17124432	0.84[GIH][hapmap]
rs3741562	0.84[GIH][hapmap]
rs376184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs393848	0.80[ASN][1000 genomes]
rs404751	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs439171	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs450423	0.80[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap]
rs484951	0.80[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs56990521	0.83[EUR][1000 genomes]
rs590460	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs613066	0.80[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs685012	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs706789	0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs706794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7294618	0.84[GIH][hapmap]
rs7307230	0.84[GIH][hapmap]
rs7961065	0.84[GIH][hapmap]
rs7961112	0.84[GIH][hapmap]
rs835593	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs835594	0.82[ASN][1000 genomes]
rs836175	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs836178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836184	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs844359	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
6	esv3437172	chr12:50478110-50480658	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4898546	LASS5	cis	parietal	SCAN
rs4898546	LASS5	cis	cerebellum	SCAN
rs4898546	AQP6	cis	parietal	SCAN
rs4898546	SNORA2A	cis	parietal	SCAN
rs4898546	ATF1	cis	parietal	SCAN
rs4898546	CERS5	cis	Nerve Tibial	GTEx
rs4898546	SLC38A1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50477800-50479400	Active TSS	Dnd41	blood
2	chr12:50478000-50478600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:50478000-50478800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:50478000-50479600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr12:50478000-50480200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:50478200-50478600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:50478200-50478600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr12:50478200-50478600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr12:50478200-50478600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:50478200-50478600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr12:50478200-50478600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr12:50478200-50478600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:50478200-50478600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:50478200-50478600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr12:50478200-50478600	Flanking Active TSS	Fetal Intestine Small	intestine
16	chr12:50478200-50478600	Enhancers	Gastric	stomach
17	chr12:50478200-50478600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr12:50478200-50478600	Enhancers	Spleen	Spleen
19	chr12:50478200-50478600	Flanking Active TSS	Hela-S3	cervix
20	chr12:50478200-50478800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:50478200-50478800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:50478200-50478800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:50478200-50478800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr12:50478200-50478800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr12:50478200-50478800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:50478200-50478800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr12:50478200-50478800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:50478200-50478800	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr12:50478200-50478800	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr12:50478200-50478800	Flanking Active TSS	Placenta	Placenta
31	chr12:50478200-50478800	Flanking Active TSS	Fetal Thymus	thymus
32	chr12:50478200-50478800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr12:50478200-50478800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr12:50478200-50478800	Flanking Active TSS	HUVEC	blood vessel
35	chr12:50478200-50478800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr12:50478200-50478800	Flanking Active TSS	NH-A	brain
37	chr12:50478200-50478800	Flanking Active TSS	Osteobl	bone
38	chr12:50478200-50479000	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr12:50478200-50479000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:50478200-50479400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:50478200-50479400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:50478200-50479600	Active TSS	Aorta	Aorta
43	chr12:50478200-50479600	Active TSS	Colonic Mucosa	Colon
44	chr12:50478200-50479600	Active TSS	Colon Smooth Muscle	Colon
45	chr12:50478200-50479600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr12:50478200-50479600	Active TSS	Pancreas	Pancrea
47	chr12:50478200-50479600	Active TSS	A549	lung
48	chr12:50478200-50479600	Active TSS	HepG2	liver
49	chr12:50478200-50479600	Active TSS	HMEC	breast
50	chr12:50478200-50479600	Active TSS	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links