Variant report

Variant	rs12812141
Chromosome Location	chr12:31516511-31516512
allele	C/T
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	MXI1	chr12:31515067-31516539	HepG2	liver:	n/a	n/a
2	SMC3	chr12:31516435-31516637	HepG2	liver:	n/a	n/a
3	CTCF	chr12:31516500-31516650	HepG2	liver:	n/a	n/a
4	CTCF	chr12:31516480-31516630	GM12873	blood:	n/a	n/a
5	HNF4A	chr12:31516470-31516655	HepG2	liver:	n/a	n/a
6	HEY1	chr12:31516384-31516717	HepG2	liver:	n/a	n/a
7	MAX	chr12:31516438-31516776	HepG2	liver:	n/a	n/a
8	RAD21	chr12:31515001-31516780	H1-hESC	embryonic stem cell:	n/a	chr12:31516223-31516235
9	STAT1	chr12:31516055-31516564	GM12878	blood:	n/a	n/a
10	CTCF	chr12:31516440-31516590	GM12872	blood:	n/a	n/a
11	CTCF	chr12:31516440-31516590	Caco-2	colon:	n/a	n/a
12	MTA3	chr12:31515285-31516523	GM12878	blood:	n/a	n/a
13	MYC	chr12:31515090-31516633	NB4	blood:	n/a	chr12:31516134-31516144 chr12:31515383-31515393
14	MAX	chr12:31514916-31516633	NB4	blood:	n/a	chr12:31516134-31516144 chr12:31515383-31515393
15	MAX	chr12:31514804-31516534	ECC-1	luminal epithelium:	n/a	chr12:31516134-31516144 chr12:31515383-31515393
16	MXI1	chr12:31515585-31516561	GM12878	blood:	n/a	n/a
17	CTCF	chr12:31516460-31516610	GM12872	blood:	n/a	n/a
18	MAX	chr12:31514937-31516853	HepG2	liver:	n/a	chr12:31516134-31516144 chr12:31515383-31515393
19	SIN3A	chr12:31514993-31516550	H1-hESC	embryonic stem cell:	n/a	chr12:31516107-31516116 chr12:31515307-31515321 chr12:31515370-31515379
20	RAD21	chr12:31516001-31516544	HCT-116	colon:	n/a	chr12:31516223-31516235
21	CTCF	chr12:31516460-31516610	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31424984..31425698-chr12:31516137..31516810,2	MCF-7	breast:
2	chr12:31512202..31513960-chr12:31515400..31517453,2	MCF-7	breast:
3	chr12:31476716..31479416-chr12:31514975..31518554,5	K562	blood:
4	chr12:31477240..31480202-chr12:31513504..31517911,10	MCF-7	breast:
5	chr12:31476716..31479352-chr12:31516399..31518554,2	K562	blood:
6	chr12:31478362..31480106-chr12:31515501..31517473,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DENND5B-1	chr12:31516415-31516729	ENSG00000256232

Variant related genes	Relation type
RNU6-318P	TF binding region
ENSG00000139146	Chromatin interaction
ENSG00000177340	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1038066	0.82[CEU][hapmap]
rs12812075	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs12816170	1.00[ASN][1000 genomes]
rs12816386	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818749	0.91[CEU][hapmap]
rs12820294	0.91[CEU][hapmap]
rs12821808	0.90[CEU][hapmap];1.00[ASN][1000 genomes]
rs12822601	1.00[ASN][1000 genomes]
rs12831480	1.00[ASN][1000 genomes]
rs17497517	0.91[CEU][hapmap]
rs17497656	0.86[CEU][hapmap]
rs1879398	0.82[AMR][1000 genomes]
rs1879399	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126897	0.91[CEU][hapmap]
rs34007930	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34184789	1.00[ASN][1000 genomes]
rs34450466	1.00[ASN][1000 genomes]
rs34585237	1.00[ASN][1000 genomes]
rs34642866	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34949976	1.00[ASN][1000 genomes]
rs34955459	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35029695	1.00[ASN][1000 genomes]
rs35692484	1.00[ASN][1000 genomes]
rs4931485	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931498	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs4931503	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs4931504	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs4931510	0.91[CEU][hapmap]
rs55771933	1.00[ASN][1000 genomes]
rs56183451	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234529	1.00[ASN][1000 genomes]
rs56327034	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66479670	1.00[ASN][1000 genomes]
rs66520413	1.00[ASN][1000 genomes]
rs66552209	1.00[ASN][1000 genomes]
rs66635949	1.00[ASN][1000 genomes]
rs67963293	1.00[ASN][1000 genomes]
rs68030436	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455661	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71455668	1.00[ASN][1000 genomes]
rs71455669	1.00[ASN][1000 genomes]
rs73080503	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31480000-31522800	Weak transcription	Right Atrium	heart
2	chr12:31514800-31516600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:31514800-31517200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr12:31514800-31517200	Enhancers	Fetal Intestine Large	intestine
5	chr12:31514800-31517400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:31514800-31518200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:31515000-31516600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr12:31515000-31517200	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:31515000-31517200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:31515000-31517200	Enhancers	Fetal Intestine Small	intestine
11	chr12:31515000-31517200	Enhancers	Fetal Kidney	kidney
12	chr12:31515200-31516600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr12:31515200-31516600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr12:31515200-31516800	Enhancers	A549	lung
15	chr12:31515400-31516600	Enhancers	Primary B cells from cord blood	blood
16	chr12:31515400-31516600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:31515400-31516600	Flanking Active TSS	GM12878-XiMat	blood
18	chr12:31515400-31516800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr12:31515400-31517200	Enhancers	Dnd41	blood
20	chr12:31515400-31518200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:31515600-31516600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:31515600-31516600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr12:31515600-31516600	Enhancers	Thymus	Thymus
24	chr12:31515600-31516800	Enhancers	Stomach Mucosa	stomach
25	chr12:31515600-31517000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:31515600-31517200	Enhancers	Primary hematopoietic stem cells	blood
27	chr12:31515600-31522400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:31515600-31522800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:31515800-31516600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:31515800-31516600	Enhancers	Placenta	Placenta
31	chr12:31515800-31517200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr12:31515800-31522800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:31516000-31516600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:31516000-31516600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:31516000-31516600	Flanking Active TSS	HepG2	liver
36	chr12:31516000-31516800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr12:31516000-31516800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr12:31516000-31516800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr12:31516000-31516800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:31516000-31516800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:31516000-31516800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr12:31516000-31516800	Enhancers	Colonic Mucosa	Colon
43	chr12:31516000-31517000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:31516000-31517000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:31516000-31517200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:31516000-31517200	Enhancers	Fetal Thymus	thymus
47	chr12:31516000-31517400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr12:31516000-31517400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:31516000-31521800	Weak transcription	Fetal Lung	lung
50	chr12:31516000-31521800	Weak transcription	Hela-S3	cervix

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