Variant report

Variant	rs12445596
Chromosome Location	chr16:12810684-12810685
allele	A/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	RFX5	chr16:12810582-12810843	HepG2	liver:	n/a	n/a
2	CEBPB	chr16:12810476-12810851	HepG2	liver:	n/a	n/a
3	MAZ	chr16:12810634-12810845	HepG2	liver:	n/a	n/a
4	CEBPB	chr16:12810564-12810922	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:12810653-12810723	HepG2	liver:	n/a	n/a
6	CEBPB	chr16:12810574-12810925	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12810060..12812444-chr16:12816737..12818922,2	MCF-7	breast:

Variant related genes	Relation type
MIR4718	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11075148	0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[AMR][1000 genomes]
rs11075151	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs12443898	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12444818	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs12445723	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12446541	0.81[ASN][1000 genomes]
rs12446858	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12447643	0.88[CEU][hapmap]
rs13332084	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72779045	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72779047	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72779050	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72779056	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72779059	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72779063	0.88[ASN][1000 genomes]
rs72779072	0.85[ASN][1000 genomes]
rs8044840	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9922287	0.85[AMR][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	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1053617	chr16:12730958-12871639	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv869284	chr16:12735729-13533462	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription 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 miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1052802	chr16:12766360-12964248	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12445596	CPPED1	cis	parietal	SCAN
rs12445596	MPV17L	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12753400-12836000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr16:12758400-12818200	Weak transcription	Left Ventricle	heart
3	chr16:12758600-12822400	Weak transcription	HSMMtube	muscle
4	chr16:12780000-12812800	Weak transcription	NH-A	brain
5	chr16:12784400-12815200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr16:12797600-12823200	Weak transcription	Primary T cells from cord blood	blood
7	chr16:12798400-12825800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr16:12798600-12822800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr16:12798600-12825800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr16:12798600-12836800	Weak transcription	Placenta	Placenta
11	chr16:12798800-12810800	Weak transcription	Esophagus	oesophagus
12	chr16:12798800-12814000	Weak transcription	Liver	Liver
13	chr16:12798800-12815200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr16:12798800-12816200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr16:12798800-12817000	Weak transcription	Aorta	Aorta
16	chr16:12798800-12817200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr16:12798800-12817600	Weak transcription	Fetal Stomach	stomach
18	chr16:12798800-12826600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr16:12799000-12816600	Weak transcription	Fetal Intestine Small	intestine
20	chr16:12799000-12817400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr16:12799000-12820200	Weak transcription	Ovary	ovary
22	chr16:12799000-12823600	Weak transcription	Adipose Nuclei	Adipose
23	chr16:12799200-12821400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr16:12799400-12823000	Weak transcription	Fetal Intestine Large	intestine
25	chr16:12801000-12815000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr16:12801400-12814800	Weak transcription	Brain Substantia Nigra	brain
27	chr16:12801600-12813200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr16:12801800-12816400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr16:12803800-12822400	Weak transcription	Spleen	Spleen
30	chr16:12806200-12818000	Weak transcription	Lung	lung
31	chr16:12808800-12810800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:12808800-12817800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr16:12809200-12821800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr16:12809400-12817000	Weak transcription	HSMM	muscle
35	chr16:12809800-12810800	Enhancers	Brain Hippocampus Middle	brain
36	chr16:12809800-12814000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr16:12810000-12810800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr16:12810200-12810800	Enhancers	Brain Cingulate Gyrus	brain
39	chr16:12810200-12811000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr16:12810200-12811000	Genic enhancers	HepG2	liver
41	chr16:12810200-12812000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr16:12810400-12811000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr16:12810400-12813800	Weak transcription	Brain Angular Gyrus	brain
44	chr16:12810600-12815000	Weak transcription	Brain Inferior Temporal Lobe	brain

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