Variant report

Variant	rs12977854
Chromosome Location	chr19:45195839-45195840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45195823..45197578-chr19:45220887..45222475,2	MCF-7	breast:
2	chr19:45188654..45190939-chr19:45193804..45196138,2	K562	blood:
3	chr19:45195689..45197488-chr19:45256706..45258285,2	MCF-7	breast:
4	chr19:45193090..45195982-chr19:45196210..45199723,4	MCF-7	breast:
5	chr19:45193034..45198920-chr19:45224756..45231512,9	MCF-7	breast:
6	chr19:45188830..45190477-chr19:45195576..45198306,2	K562	blood:
7	chr19:45193665..45201150-chr19:45248511..45253202,11	MCF-7	breast:
8	chr19:45189167..45190891-chr19:45195499..45197736,2	MCF-7	breast:
9	chr19:45195121..45197264-chr19:45199908..45201765,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEACAM16-2	chr19:45195051-45196353	NONHSAT066710

No data

Variant related genes	Relation type
ENSG00000266903	Chromatin interaction
ENSG00000252200	Chromatin interaction
ENSG00000069399	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs34830633	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35401363	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803741	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61458713	1.00[ASN][1000 genomes]
rs62119329	1.00[ASN][1000 genomes]
rs62120564	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046432	1.00[ASN][1000 genomes]
rs73561940	1.00[ASN][1000 genomes]
rs73561943	1.00[ASN][1000 genomes]
rs73561968	1.00[ASN][1000 genomes]
rs74172479	1.00[ASN][1000 genomes]
rs8107008	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs930462	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062812	chr19:45042262-45214796	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv912116	chr19:45146103-45298069	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv9737	chr19:45178110-45206629	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12977854	ZNF528	cis	cerebellum	SCAN
rs12977854	KLK15	cis	parietal	SCAN
rs12977854	ZNF611	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45166000-45197400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:45181600-45198800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:45192400-45202000	Enhancers	Liver	Liver
4	chr19:45193000-45200200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr19:45193000-45200600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:45193600-45197600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:45194400-45196200	Enhancers	Primary B cells from peripheral blood	blood
8	chr19:45194400-45196400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:45194600-45196200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr19:45194600-45196400	Enhancers	Primary hematopoietic stem cells	blood
11	chr19:45194600-45196400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:45194600-45196600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr19:45194800-45196000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr19:45194800-45196200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:45194800-45196200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:45194800-45196200	Enhancers	Stomach Mucosa	stomach
17	chr19:45194800-45196200	Flanking Active TSS	A549	lung
18	chr19:45194800-45196400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:45194800-45196600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr19:45194800-45196600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:45194800-45196600	Enhancers	Duodenum Mucosa	Duodenum
22	chr19:45194800-45196600	Enhancers	HUVEC	blood vessel
23	chr19:45194800-45196800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:45194800-45198000	Enhancers	Spleen	Spleen
25	chr19:45194800-45199600	Enhancers	Fetal Intestine Large	intestine
26	chr19:45195000-45196000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:45195000-45196000	Enhancers	Primary B cells from cord blood	blood
28	chr19:45195000-45196000	Enhancers	Primary T cells from cord blood	blood
29	chr19:45195000-45196000	Flanking Active TSS	Hela-S3	cervix
30	chr19:45195000-45196000	Enhancers	HSMMtube	muscle
31	chr19:45195000-45196000	Enhancers	NHDF-Ad	bronchial
32	chr19:45195000-45196200	Enhancers	HMEC	breast
33	chr19:45195000-45196200	Enhancers	HSMM	muscle
34	chr19:45195000-45196400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:45195000-45196400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:45195000-45196400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:45195000-45196400	Enhancers	NH-A	brain
38	chr19:45195000-45200600	Enhancers	Fetal Intestine Small	intestine
39	chr19:45195000-45202200	Enhancers	Pancreas	Pancrea
40	chr19:45195200-45196000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr19:45195200-45196200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr19:45195200-45196400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:45195400-45196000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr19:45195400-45196200	Enhancers	Adipose Nuclei	Adipose
45	chr19:45195400-45196200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr19:45195400-45196400	Enhancers	Fetal Heart	heart
47	chr19:45195400-45197200	Weak transcription	Colonic Mucosa	Colon
48	chr19:45195400-45197400	Weak transcription	Gastric	stomach
49	chr19:45195600-45196000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:45195600-45197200	Weak transcription	K562	blood

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