Variant report

Variant	rs9927063
Chromosome Location	chr16:12852671-12852672
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	NFATC1	chr16:12852255-12852704	GM12878	blood:	n/a	n/a
2	GATA2	chr16:12851413-12852860	SH-SY5Y	brain:	n/a	chr16:12851953-12851963
3	KAP1	chr16:12851787-12852693	HEK293	kidney:	n/a	n/a
4	EP300	chr16:12850870-12853459	SK-N-SH	brain:	n/a	n/a
5	BHLHE40	chr16:12851969-12852752	K562	blood:	n/a	n/a
6	ATF1	chr16:12851970-12852717	K562	blood:	n/a	n/a
7	MXI1	chr16:12851000-12853658	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr16:12851764-12852725	SK-N-SH	brain:	n/a	chr16:12851953-12851963
9	POLR2A	chr16:12852177-12852980	K562	blood:	n/a	n/a
10	KAP1	chr16:12851559-12852839	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12837397..12840292-chr16:12850360..12852909,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SHISA9-1	chr16:12851346-12853272	NONHSAT140631
2	lnc-SHISA9-1	chr16:12851346-12853272	NONHSAT140630

Variant related genes	Relation type
ENSG00000261158	TF binding region
ENSG00000260378	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13332101	1.00[AMR][1000 genomes]
rs13333158	1.00[AMR][1000 genomes]
rs13334654	1.00[AMR][1000 genomes]
rs60209758	1.00[AMR][1000 genomes]
rs62029680	1.00[AMR][1000 genomes]
rs9922426	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926045	1.00[AMR][1000 genomes]
rs9933205	1.00[AMR][1000 genomes]
rs9939974	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv1036493	chr16:12817416-12881078	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
10	esv2751547	chr16:12817920-12882336	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
11	esv2751548	chr16:12817920-12892036	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
12	nsv1052892	chr16:12824219-12881078	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
13	nsv525286	chr16:12826785-12878592	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv571480	chr16:12826785-12878592	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	nsv571481	chr16:12826785-12880446	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
16	esv2751549	chr16:12829006-12880446	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9927063	CPPED1	cis	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12834800-12873600	Weak transcription	Aorta	Aorta
2	chr16:12835600-12863400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:12835600-12865200	Weak transcription	Ovary	ovary
4	chr16:12835600-12869800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr16:12839200-12863600	Weak transcription	Fetal Intestine Large	intestine
6	chr16:12839200-12869000	Weak transcription	Primary B cells from cord blood	blood
7	chr16:12839600-12854400	Weak transcription	Fetal Intestine Small	intestine
8	chr16:12839600-12865000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr16:12839600-12873600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr16:12846800-12856200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr16:12847600-12865000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr16:12848000-12853400	Enhancers	Liver	Liver
13	chr16:12848000-12858400	Weak transcription	Gastric	stomach
14	chr16:12848200-12857000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr16:12848600-12854200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr16:12849000-12853600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:12849200-12865000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr16:12849600-12865000	Weak transcription	Osteobl	bone
19	chr16:12850200-12876400	Weak transcription	Primary T cells from cord blood	blood
20	chr16:12850400-12853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr16:12850400-12864000	Weak transcription	Esophagus	oesophagus
22	chr16:12850600-12853200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:12850800-12853600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr16:12850800-12854400	Enhancers	Brain Substantia Nigra	brain
25	chr16:12851000-12853800	Enhancers	Brain Angular Gyrus	brain
26	chr16:12851000-12854000	Enhancers	Brain Cingulate Gyrus	brain
27	chr16:12851000-12855200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr16:12851200-12852800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr16:12851200-12853400	Enhancers	Right Atrium	heart
30	chr16:12851200-12853800	Enhancers	Brain Anterior Caudate	brain
31	chr16:12851200-12853800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr16:12851200-12854000	Genic enhancers	HepG2	liver
33	chr16:12851200-12854400	Enhancers	Brain Hippocampus Middle	brain
34	chr16:12851200-12855800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr16:12851400-12852800	Enhancers	HUVEC	blood vessel
36	chr16:12851400-12853400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr16:12851600-12852800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr16:12851600-12852800	Enhancers	K562	blood
39	chr16:12851800-12860800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr16:12852000-12853200	Enhancers	Placenta	Placenta
41	chr16:12852000-12853400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr16:12852000-12853400	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr16:12852200-12853000	Enhancers	GM12878-XiMat	blood
44	chr16:12852200-12853400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr16:12852200-12853400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr16:12852200-12853400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr16:12852200-12857600	Weak transcription	Left Ventricle	heart
48	chr16:12852200-12868400	Weak transcription	Adipose Nuclei	Adipose
49	chr16:12852200-12896600	Weak transcription	Right Ventricle	heart
50	chr16:12852400-12852800	Genic enhancers	Muscle Satellite Cultured Cells	--

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