Variant report

Variant	rs10880962
Chromosome Location	chr12:46773444-46773445
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr12:46773241-46773529	K562	blood:	n/a	n/a
2	TBL1XR1	chr12:46773239-46773558	K562	blood:	n/a	n/a
3	RCOR1	chr12:46773367-46773492	K562	blood:	n/a	n/a
4	ARID3A	chr12:46773332-46773608	K562	blood:	n/a	n/a
5	IRF1	chr12:46773306-46773546	K562	blood:	n/a	n/a
6	JUN	chr12:46773256-46773552	K562	blood:	n/a	n/a
7	IRF1	chr12:46773210-46773584	K562	blood:	n/a	n/a
8	TEAD4	chr12:46773167-46773609	K562	blood:	n/a	n/a
9	BACH1	chr12:46773442-46773450	K562	blood:	n/a	n/a
10	ATF1	chr12:46773238-46773546	K562	blood:	n/a	n/a
11	EP300	chr12:46773187-46773657	K562	blood:	n/a	chr12:46773624-46773638 chr12:46773622-46773636
12	ZMIZ1	chr12:46773347-46773482	K562	blood:	n/a	n/a
13	RCOR1	chr12:46773239-46773612	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46772586..46775083-chr12:47057146..47059153,2	MCF-7	breast:
2	chr12:46771601..46773692-chr12:46823826..46825790,2	K562	blood:
3	chr12:46772190..46774754-chr12:46865933..46867665,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC38A2-1	chr12:46773050-46773561	NONHSAT027862

No data

Variant related genes	Relation type
ENSG00000257261	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10785620	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10785624	0.94[EUR][1000 genomes]
rs11183468	0.85[CEU][hapmap]
rs12296120	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12307969	0.87[EUR][1000 genomes]
rs12320197	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1873793	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279559	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2408497	0.82[CEU][hapmap]
rs2897968	0.85[CEU][hapmap]
rs35377637	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4076248	0.85[CEU][hapmap]
rs6582656	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7487075	0.85[CEU][hapmap]
rs7972573	0.82[AMR][1000 genomes]
rs7976280	0.80[JPT][hapmap]
rs7979418	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46767800-46773800	Weak transcription	Pancreas	Pancrea
2	chr12:46767800-46774000	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:46767800-46774600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:46767800-46776200	Weak transcription	Small Intestine	intestine
5	chr12:46768000-46775600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:46768000-46776200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:46768000-46776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:46768000-46776200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:46768000-46776200	Weak transcription	Brain Substantia Nigra	brain
10	chr12:46768000-46776200	Weak transcription	Placenta	Placenta
11	chr12:46768000-46776200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:46768000-46776400	Weak transcription	Gastric	stomach
13	chr12:46768000-46776400	Weak transcription	Left Ventricle	heart
14	chr12:46768000-46776400	Weak transcription	Psoas Muscle	Psoas
15	chr12:46768200-46773800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:46768200-46775800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:46768200-46776000	Weak transcription	NH-A	brain
18	chr12:46768400-46773600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:46768400-46775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:46768400-46775800	Weak transcription	A549	lung
21	chr12:46768400-46776000	Weak transcription	NHEK	skin
22	chr12:46768400-46776200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr12:46768400-46776200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr12:46768400-46776400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:46768600-46775800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:46768600-46776200	Weak transcription	Thymus	Thymus
27	chr12:46768800-46773800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:46768800-46774000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:46768800-46775600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:46768800-46775600	Weak transcription	NHLF	lung
31	chr12:46768800-46776000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:46768800-46776200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:46768800-46776200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:46769200-46774000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:46769200-46776000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:46769200-46776200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:46769200-46776400	Weak transcription	Primary T cells from cord blood	blood
38	chr12:46770800-46775600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:46771000-46776200	Weak transcription	Liver	Liver
40	chr12:46771000-46776200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:46771200-46773600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:46772000-46776000	Weak transcription	NHDF-Ad	bronchial
43	chr12:46772200-46774000	Weak transcription	HepG2	liver
44	chr12:46772200-46776000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:46772200-46776400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:46772800-46774600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:46772800-46775600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:46772800-46775600	Weak transcription	Hela-S3	cervix
49	chr12:46772800-46776200	Weak transcription	Primary B cells from cord blood	blood
50	chr12:46773000-46774800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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