Variant report

Variant	rs12302334
Chromosome Location	chr12:123461080-123461081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123458534-123466263	K562	blood:	n/a	n/a
2	POLR2A	chr12:123458680-123461169	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:123458851-123461232	K562	blood:	n/a	n/a
4	POLR2A	chr12:123458643-123461407	HL-60	blood:	n/a	n/a
5	POLR2A	chr12:123460872-123461345	HepG2	liver:	n/a	n/a
6	TEAD4	chr12:123458672-123461113	K562	blood:	n/a	n/a
7	POLR2A	chr12:123460287-123466106	K562	blood:	n/a	n/a
8	POLR2A	chr12:123458558-123461092	PANC-1	pancreas:	n/a	n/a
9	JUN	chr12:123458446-123461591	K562	blood:	n/a	chr12:123460542-123460551
10	POLR2A	chr12:123458769-123461278	PFSK-1	brain:	n/a	n/a
11	HEY1	chr12:123458854-123461109	K562	blood:	n/a	n/a
12	POLR2A	chr12:123458662-123461154	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:123458588-123461084	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr12:123458525-123461675	K562	blood:	n/a	n/a
15	POLR2A	chr12:123458736-123461084	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:123459054..123462367-chr12:123715409..123720380,5	K562	blood:
2	chr12:123458147..123462549-chr12:123715608..123720287,8	MCF-7	breast:
3	chr12:120728398..120730404-chr12:123459731..123462257,2	MCF-7	breast:
4	chr12:123433587..123436454-chr12:123458977..123461529,2	K562	blood:
5	chr12:123344929..123347895-chr12:123458197..123461633,3	MCF-7	breast:
6	chr12:123457894..123461734-chr12:123715409..123718960,7	K562	blood:
7	chr12:123353599..123356535-chr12:123459324..123461652,2	MCF-7	breast:

No data

Variant related genes	Relation type
OGFOD2	TF binding region
ARL6IP4	TF binding region
ABCB9	TF binding region
ENSG00000150967	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10466866	1.00[CEU][hapmap]
rs10846469	0.82[MEX][hapmap]
rs10846471	0.82[MEX][hapmap]
rs10848148	1.00[CHD][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs10848291	0.83[AMR][1000 genomes]
rs10848363	0.83[AMR][1000 genomes]
rs10848365	1.00[CHD][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs10848429	0.91[AMR][1000 genomes]
rs11057175	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11060273	1.00[EUR][1000 genomes]
rs11060888	0.83[AMR][1000 genomes]
rs11061166	0.83[AMR][1000 genomes]
rs11061589	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11061601	0.91[AMR][1000 genomes]
rs11061611	1.00[CHD][hapmap];0.82[MEX][hapmap]
rs11061614	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12306711	1.00[CHD][hapmap];0.91[AMR][1000 genomes]
rs12311043	1.00[CHD][hapmap]
rs12318389	0.82[MEX][hapmap]
rs12318594	1.00[CHD][hapmap];0.82[MEX][hapmap]
rs12319324	1.00[CEU][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv899578	chr12:123459005-123474529	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr12:123458400-123461200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:123459800-123461400	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr12:123459800-123461400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:123459800-123461600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
5	chr12:123460000-123461400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:123460000-123461400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:123460000-123461400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr12:123460000-123461400	Flanking Active TSS	Liver	Liver
9	chr12:123460200-123461200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:123460200-123461200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:123460200-123461200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:123460200-123461200	Flanking Active TSS	Brain Angular Gyrus	brain
13	chr12:123460200-123461200	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr12:123460200-123461200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr12:123460200-123461200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:123460200-123461200	Flanking Active TSS	Fetal Muscle Leg	muscle
17	chr12:123460200-123461200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr12:123460200-123461200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr12:123460200-123461200	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr12:123460200-123461200	Flanking Active TSS	Hela-S3	cervix
21	chr12:123460200-123461200	Flanking Active TSS	K562	blood
22	chr12:123460200-123461400	Flanking Active TSS	Colonic Mucosa	Colon
23	chr12:123460200-123461400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr12:123460200-123461600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:123460200-123461600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:123460200-123461600	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr12:123460400-123461200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:123460400-123461200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:123460400-123461200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr12:123460400-123461200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr12:123460400-123461200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr12:123460400-123461200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:123460400-123461200	Flanking Active TSS	Dnd41	blood
34	chr12:123460400-123461200	Flanking Active TSS	HSMM	muscle
35	chr12:123460400-123461200	Flanking Active TSS	NHEK	skin
36	chr12:123460400-123461200	Flanking Active TSS	Osteobl	bone
37	chr12:123460400-123461400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:123460400-123461400	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr12:123460400-123461400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr12:123460400-123461400	Flanking Active TSS	GM12878-XiMat	blood
41	chr12:123460400-123461400	Flanking Active TSS	HMEC	breast
42	chr12:123460600-123461200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:123460600-123461200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:123460600-123461200	Enhancers	Ovary	ovary
45	chr12:123460600-123461200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr12:123460600-123461400	Enhancers	Right Atrium	heart
47	chr12:123460600-123461400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr12:123460600-123461400	Flanking Active TSS	HepG2	liver
49	chr12:123460600-123461600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:123460600-123461600	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links