Variant report

Variant	rs7488942
Chromosome Location	chr12:48162480-48162481
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:93)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:93 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr12:48162197-48162677	MCF-7	breast:	n/a	chr12:48162467-48162476
2	ZNF217	chr12:48162173-48162551	MCF-7	breast:	n/a	n/a
3	MAX	chr12:48162200-48162615	Hela-S3	cervix:	n/a	n/a
4	NR2F2	chr12:48162117-48162763	MCF-7	breast:	n/a	n/a
5	TEAD4	chr12:48162156-48162564	A549	lung:	n/a	chr12:48162467-48162476
6	JUND	chr12:48162019-48162708	T-47D	breast:	n/a	n/a
7	EP300	chr12:48162012-48163165	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr12:48162215-48162599	Hela-S3	cervix:	n/a	n/a
9	NR3C1	chr12:48162173-48162650	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr12:48162129-48162685	HepG2	liver:	n/a	chr12:48162467-48162476
11	GATA3	chr12:48161999-48162786	MCF-7	breast:	n/a	n/a
12	GTF2F1	chr12:48162155-48162597	Hela-S3	cervix:	n/a	n/a
13	ESR1	chr12:48162057-48162745	ECC-1	luminal epithelium:	n/a	n/a
14	TEAD4	chr12:48162114-48162627	MCF-7	breast:	n/a	chr12:48162467-48162476
15	HDAC2	chr12:48162115-48162674	MCF-7	breast:	n/a	n/a
16	TEAD4	chr12:48162130-48162767	A549	lung:	n/a	chr12:48162467-48162476
17	NR2F2	chr12:48162052-48162719	MCF-7	breast:	n/a	n/a
18	TEAD4	chr12:48162264-48162612	H1-hESC	embryonic stem cell:	n/a	chr12:48162467-48162476
19	GATA3	chr12:48162204-48162552	MCF-7	breast:	n/a	n/a
20	FOXM1	chr12:48161991-48163278	ECC-1	luminal epithelium:	n/a	n/a
21	STAT3	chr12:48162231-48162638	MCF10A-Er-Src	breast:	n/a	n/a
22	FOXA1	chr12:48162095-48162567	HepG2	liver:	n/a	n/a
23	ATF1	chr12:48162230-48162585	K562	blood:	n/a	n/a
24	FOXM1	chr12:48161951-48162940	ECC-1	luminal epithelium:	n/a	n/a
25	FOXA1	chr12:48162170-48162565	T-47D	breast:	n/a	n/a
26	SP1	chr12:48162055-48162753	A549	lung:	n/a	n/a
27	SP1	chr12:48162026-48162701	A549	lung:	n/a	n/a
28	FOXM1	chr12:48162006-48162578	MCF-7	breast:	n/a	n/a
29	SIN3AK20	chr12:48162056-48162733	MCF-7	breast:	n/a	n/a
30	ESR1	chr12:48161991-48162789	ECC-1	luminal epithelium:	n/a	n/a
31	MAZ	chr12:48162221-48162574	Hela-S3	cervix:	n/a	n/a
32	TEAD4	chr12:48162012-48163611	ECC-1	luminal epithelium:	n/a	chr12:48162467-48162476
33	MAX	chr12:48161970-48162718	ECC-1	luminal epithelium:	n/a	n/a
34	TCF12	chr12:48161962-48162862	ECC-1	luminal epithelium:	n/a	n/a
35	FOXA1	chr12:48162132-48162563	HepG2	liver:	n/a	n/a
36	FOXA2	chr12:48162128-48162494	HepG2	liver:	n/a	n/a
37	REST	chr12:48162236-48162641	MCF-7	breast:	n/a	n/a
38	GATA3	chr12:48162163-48162639	T-47D	breast:	n/a	n/a
39	FOXA2	chr12:48162035-48162557	A549	lung:	n/a	n/a
40	RFX5	chr12:48162140-48162598	Hela-S3	cervix:	n/a	n/a
41	FOXA1	chr12:48162040-48162564	ECC-1	luminal epithelium:	n/a	n/a
42	ARID3A	chr12:48162308-48162680	HepG2	liver:	n/a	n/a
43	RCOR1	chr12:48162206-48162650	Hela-S3	cervix:	n/a	n/a
44	ESR1	chr12:48162091-48162657	ECC-1	luminal epithelium:	n/a	n/a
45	GATA3	chr12:48162142-48162574	T-47D	breast:	n/a	n/a
46	CHD2	chr12:48162190-48162570	Hela-S3	cervix:	n/a	n/a
47	EP300	chr12:48162174-48162623	Hela-S3	cervix:	n/a	n/a
48	EP300	chr12:48161960-48163160	ECC-1	luminal epithelium:	n/a	n/a
49	EP300	chr12:48162043-48162765	A549	lung:	n/a	n/a
50	TEAD4	chr12:48162241-48162630	K562	blood:	n/a	chr12:48162467-48162476

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48109440..48111466-chr12:48162324..48164049,2	MCF-7	breast:
2	chr12:48161664..48163329-chr12:48225298..48227040,2	MCF-7	breast:
3	chr12:48143657..48146217-chr12:48161710..48163249,2	MCF-7	breast:
4	chr12:48152002..48153917-chr12:48162082..48164743,2	MCF-7	breast:
5	chr12:48159584..48163240-chr12:48212349..48215466,3	MCF-7	breast:
6	chr12:48151780..48155631-chr12:48159603..48164338,5	MCF-7	breast:
7	chr12:48139406..48141330-chr12:48160629..48162925,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM106C-6	chr12:48162312-48163014	NONHSAT027943

No data

Variant related genes	Relation type
SLC48A1	TF binding region
ENSG00000111405	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000257433	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1006476	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1006477	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58067800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59205218	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60776348	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7135791	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7136720	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7306788	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7307367	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73291230	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs734706	0.89[GIH][hapmap]
rs7959510	0.94[CEU][hapmap];0.85[GIH][hapmap]
rs7964310	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer 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	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7488942	BCDIN3D	cis	cerebellum	SCAN
rs7488942	OR5D13	trans	parietal	SCAN
rs7488942	RAPGEF3	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48153600-48162800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:48153600-48166000	Weak transcription	Brain Angular Gyrus	brain
3	chr12:48153600-48166200	Weak transcription	Brain Anterior Caudate	brain
4	chr12:48153600-48166400	Weak transcription	Fetal Brain Female	brain
5	chr12:48153600-48166800	Weak transcription	Gastric	stomach
6	chr12:48153800-48165600	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:48153800-48165800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:48153800-48166200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:48154400-48165800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:48156800-48163400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:48157600-48164200	Weak transcription	Fetal Lung	lung
12	chr12:48157800-48165800	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:48157800-48166200	Weak transcription	Lung	lung
14	chr12:48157800-48166200	Weak transcription	Right Atrium	heart
15	chr12:48158200-48164800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:48158200-48166600	Weak transcription	Fetal Kidney	kidney
17	chr12:48158400-48163800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr12:48158400-48164400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:48158600-48164800	Enhancers	NHEK	skin
20	chr12:48159200-48162600	Enhancers	Thymus	Thymus
21	chr12:48159200-48162800	Weak transcription	Esophagus	oesophagus
22	chr12:48159400-48166600	Weak transcription	Colonic Mucosa	Colon
23	chr12:48159800-48166400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:48159800-48166600	Weak transcription	Right Ventricle	heart
25	chr12:48160200-48164000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:48160400-48166200	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:48160600-48162800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:48160600-48163200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:48160800-48163800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:48160800-48164000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:48160800-48164000	Enhancers	HSMM	muscle
32	chr12:48160800-48164400	Enhancers	Placenta	Placenta
33	chr12:48160800-48166000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:48161000-48163200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:48161000-48164000	Weak transcription	Primary B cells from cord blood	blood
36	chr12:48161000-48164000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:48161000-48166000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:48161000-48166200	Weak transcription	Left Ventricle	heart
39	chr12:48161200-48162800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr12:48161200-48162800	Enhancers	HUVEC	blood vessel
41	chr12:48161200-48162800	Enhancers	Osteobl	bone
42	chr12:48161200-48163000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:48161200-48164400	Enhancers	Hela-S3	cervix
44	chr12:48161200-48164400	Enhancers	HepG2	liver
45	chr12:48161200-48164400	Enhancers	HMEC	breast
46	chr12:48161200-48164600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:48161400-48163000	Enhancers	NH-A	brain
48	chr12:48161400-48164800	Enhancers	K562	blood
49	chr12:48161400-48166200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:48161400-48166400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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