Variant report

Variant	rs12981405
Chromosome Location	chr19:19651577-19651578
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19651192..19652936-chr19:19774066..19776214,2	MCF-7	breast:
2	chr19:19431326..19434090-chr19:19651434..19653911,2	K562	blood:
3	chr19:19650831..19653075-chr19:20010995..20012617,3	K562	blood:
4	chr19:19626939..19628497-chr19:19651278..19652936,2	K562	blood:
5	chr19:19649974..19652165-chr19:19739340..19740963,2	MCF-7	breast:
6	chr19:19625365..19628497-chr19:19651436..19653967,3	K562	blood:
7	chr19:19650697..19653588-chr19:19753029..19754860,3	K562	blood:
8	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:
9	chr19:19649331..19652417-chr19:19771491..19776120,6	K562	blood:
10	chr19:19649879..19653588-chr19:19753029..19755939,4	K562	blood:
11	chr19:19651405..19654732-chr19:19727842..19732175,4	MCF-7	breast:
12	chr19:19649600..19655493-chr19:19770960..19774805,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258674	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000184635	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000105717	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000267268	Chromatin interaction
ENSG00000186010	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10401193	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10402308	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10402451	0.81[ASN][1000 genomes]
rs10402627	0.82[ASN][1000 genomes]
rs10404728	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10422819	0.86[ASN][1000 genomes]
rs1047361	0.81[ASN][1000 genomes]
rs1054284	0.88[ASN][1000 genomes]
rs1054930	0.86[ASN][1000 genomes]
rs1063966	0.82[ASN][1000 genomes]
rs11669516	0.82[ASN][1000 genomes]
rs12972397	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12977524	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1465695	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16996148	0.84[AFR][1000 genomes]
rs1865034	0.81[ASN][1000 genomes]
rs2082421	0.87[ASN][1000 genomes]
rs2099333	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2163804	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2163805	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2288852	0.81[ASN][1000 genomes]
rs2304098	0.86[ASN][1000 genomes]
rs28478453	0.81[ASN][1000 genomes]
rs34647936	0.82[ASN][1000 genomes]
rs3752151	0.88[ASN][1000 genomes]
rs3794990	0.81[ASN][1000 genomes]
rs3794993	0.81[ASN][1000 genomes]
rs4808199	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4808208	0.84[ASN][1000 genomes]
rs4808960	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4808964	0.87[ASN][1000 genomes]
rs4808965	0.85[ASN][1000 genomes]
rs4808967	0.85[ASN][1000 genomes]
rs60003758	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511036	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6909	0.82[ASN][1000 genomes]
rs7245983	0.82[ASN][1000 genomes]
rs7250658	0.87[EUR][1000 genomes]
rs7250893	0.84[ASN][1000 genomes]
rs7252888	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7253807	0.85[ASN][1000 genomes]
rs751856	0.81[ASN][1000 genomes]
rs751858	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs754255	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs892021	0.81[ASN][1000 genomes]
rs892022	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv543928	chr19:19649839-19664043	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12981405	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:19648200-19651600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr19:19649800-19651600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:19649800-19651600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:19650000-19651600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:19650000-19651600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:19650200-19651600	Bivalent Enhancer	Primary B cells from cord blood	blood
9	chr19:19650400-19651600	ZNF genes & repeats	Spleen	Spleen
10	chr19:19650400-19653000	Bivalent Enhancer	Placenta	Placenta
11	chr19:19650600-19651600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr19:19650600-19652600	Enhancers	Gastric	stomach
13	chr19:19650800-19651600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:19650800-19651600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
15	chr19:19650800-19651600	Bivalent Enhancer	Fetal Brain Male	brain
16	chr19:19650800-19651600	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr19:19650800-19651800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:19650800-19652200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
19	chr19:19650800-19652200	Bivalent Enhancer	Fetal Lung	lung
20	chr19:19650800-19652400	Enhancers	Pancreas	Pancrea
21	chr19:19650800-19652600	Bivalent Enhancer	Fetal Intestine Small	intestine
22	chr19:19650800-19652800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:19650800-19652800	Enhancers	Fetal Heart	heart
24	chr19:19651000-19651800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr19:19651000-19651800	Bivalent Enhancer	Esophagus	oesophagus
26	chr19:19651000-19651800	Bivalent/Poised TSS	Psoas Muscle	Psoas
27	chr19:19651000-19652000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:19651200-19651600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr19:19651200-19651600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:19651200-19651600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:19651200-19651600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr19:19651200-19651600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr19:19651200-19652000	Flanking Active TSS	Right Atrium	heart
34	chr19:19651200-19652200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
35	chr19:19651200-19652200	Flanking Active TSS	Ovary	ovary
36	chr19:19651200-19652400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:19651200-19652400	Flanking Bivalent TSS/Enh	Thymus	Thymus
38	chr19:19651400-19651600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr19:19651400-19651600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr19:19651400-19651600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:19651400-19651600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr19:19651400-19651600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:19651400-19651600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
44	chr19:19651400-19651600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
45	chr19:19651400-19651600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
46	chr19:19651400-19651600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
47	chr19:19651400-19651600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
48	chr19:19651400-19651600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
49	chr19:19651400-19651600	Enhancers	GM12878-XiMat	blood
50	chr19:19651400-19651600	Enhancers	K562	blood

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