Variant report

Variant	rs596940
Chromosome Location	chr12:123560731-123560732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr12:123560011-123561031	MCF-7	breast:	n/a	n/a
2	MAX	chr12:123560455-123560879	GM12878	blood:	n/a	n/a
3	GATA3	chr12:123560209-123560840	T-47D	breast:	n/a	n/a
4	RAD21	chr12:123560100-123560841	MCF-7	breast:	n/a	n/a
5	HDAC2	chr12:123560218-123560794	MCF-7	breast:	n/a	chr12:123560744-123560763
6	MAX	chr12:123560248-123560958	MCF-7	breast:	n/a	n/a
7	GATA3	chr12:123560150-123560877	MCF-7	breast:	n/a	n/a
8	GATA3	chr12:123560207-123560860	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr12:123560135-123560913	MCF-7	breast:	n/a	n/a
10	MXI1	chr12:123560492-123560765	GM12878	blood:	n/a	n/a
11	HDAC2	chr12:123560168-123560779	MCF-7	breast:	n/a	chr12:123560744-123560763
12	GATA3	chr12:123560326-123560808	T-47D	breast:	n/a	n/a
13	NR2F2	chr12:123560213-123560822	MCF-7	breast:	n/a	n/a
14	FOXA1	chr12:123560401-123560734	T-47D	breast:	n/a	n/a
15	MAX	chr12:123560185-123560962	MCF-7	breast:	n/a	n/a
16	NR2F2	chr12:123560157-123560827	MCF-7	breast:	n/a	n/a
17	TCF7L2	chr12:123559998-123560921	HEK293	kidney:	n/a	chr12:123560248-123560262
18	MXI1	chr12:123560118-123561416	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123560295..123563017-chr12:123563846..123566062,3	K562	blood:
2	chr12:123558728..123560764-chr12:123563794..123566553,2	MCF-7	breast:
3	chr12:123559703..123562585-chr12:123566918..123569407,2	K562	blood:
4	chr12:123463143..123466030-chr12:123559790..123563075,3	MCF-7	breast:
5	chr12:123558968..123563276-chr12:123716606..123719909,6	MCF-7	breast:
6	chr12:123560295..123563384-chr12:123563700..123566062,4	K562	blood:

No data

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000251497	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000182196	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10847980	0.93[JPT][hapmap]
rs11057167	0.80[CEU][hapmap]
rs11060762	1.00[ASW][hapmap];0.83[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs11061244	0.80[CEU][hapmap]
rs11061615	0.80[CEU][hapmap]
rs12371718	0.80[CEU][hapmap]
rs1568918	0.85[ASN][1000 genomes]
rs2844287	0.80[CEU][hapmap]
rs3782289	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs4148857	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4148858	0.90[ASN][1000 genomes]
rs4148859	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs4148864	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4148865	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs4759359	1.00[ASW][hapmap];0.83[CEU][hapmap]
rs4759362	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs523682	0.80[CEU][hapmap]
rs73230017	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7398697	0.90[ASN][1000 genomes]
rs7967118	1.00[ASN][1000 genomes]
rs947800	0.80[CEU][hapmap]
rs947801	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	esv3421941	chr12:123556899-123561197	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs596940	OGFOD2	cis	Thyroid	GTEx
rs596940	CPLX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123542800-123563800	Enhancers	Left Ventricle	heart
2	chr12:123546400-123562400	Enhancers	Liver	Liver
3	chr12:123549600-123561000	Weak transcription	Hela-S3	cervix
4	chr12:123550000-123562400	Enhancers	Fetal Heart	heart
5	chr12:123551200-123561800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:123553800-123563800	Enhancers	Right Ventricle	heart
7	chr12:123554000-123563000	Enhancers	Right Atrium	heart
8	chr12:123554000-123563800	Enhancers	Brain Hippocampus Middle	brain
9	chr12:123555600-123561200	Weak transcription	Pancreas	Pancrea
10	chr12:123555800-123560800	Weak transcription	HUVEC	blood vessel
11	chr12:123555800-123561000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:123556400-123561200	Weak transcription	NHLF	lung
13	chr12:123556400-123562600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr12:123556600-123561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:123557400-123565600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:123557800-123561400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:123558000-123560800	Enhancers	Brain Substantia Nigra	brain
18	chr12:123558400-123561400	Enhancers	Brain Cingulate Gyrus	brain
19	chr12:123558400-123563800	Enhancers	Lung	lung
20	chr12:123558600-123561600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr12:123558600-123562400	Enhancers	Adipose Nuclei	Adipose
22	chr12:123558600-123562800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr12:123558800-123561600	Enhancers	Fetal Muscle Leg	muscle
24	chr12:123558800-123563200	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:123559000-123561000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:123559000-123561000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr12:123559000-123561000	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr12:123559000-123561400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr12:123559000-123561600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:123559000-123561600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr12:123559000-123561800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr12:123559000-123562000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:123559200-123560800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:123559200-123561400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr12:123559200-123561600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr12:123559200-123561600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr12:123559200-123561800	Enhancers	Primary B cells from peripheral blood	blood
38	chr12:123559200-123562000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr12:123559200-123562200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr12:123559400-123561000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:123559400-123561400	Enhancers	Fetal Lung	lung
42	chr12:123559400-123561400	Enhancers	HSMMtube	muscle
43	chr12:123559400-123561600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:123559400-123561600	Enhancers	HMEC	breast
45	chr12:123559400-123561600	Enhancers	NHEK	skin
46	chr12:123559400-123561800	Enhancers	Duodenum Mucosa	Duodenum
47	chr12:123559400-123562000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:123559400-123562200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:123559400-123562200	Enhancers	NHDF-Ad	bronchial
50	chr12:123559600-123560800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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