Variant report

Variant	rs1427785
Chromosome Location	chr12:106500408-106500409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106488784..106491367-chr12:106500310..106501960,2	MCF-7	breast:
2	chr12:106499587..106502262-chr12:106509960..106512334,2	MCF-7	breast:
3	chr12:106500371..106501923-chr12:106505629..106508157,2	MCF-7	breast:
4	chr12:106495439..106497630-chr12:106499867..106501572,2	MCF-7	breast:
5	chr12:106499591..106503536-chr12:106504416..106508585,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257438	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10746055	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861555	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112867	0.94[CHB][hapmap]
rs11112868	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112870	0.83[ASN][1000 genomes]
rs11112872	0.84[CHB][hapmap]
rs12371401	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1427786	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1560000	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2434082	0.85[ASN][1000 genomes]
rs2436597	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2436598	0.82[ASN][1000 genomes]
rs2468198	0.85[ASN][1000 genomes]
rs2468199	0.96[ASN][1000 genomes]
rs2569973	0.97[ASN][1000 genomes]
rs2956406	0.85[ASN][1000 genomes]
rs7131912	0.99[ASN][1000 genomes]
rs7132167	0.81[CEU][hapmap]
rs754724	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7964234	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs958422	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs967872	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832509	chr12:106363888-106516221	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1427785	CKAP4	cis	parietal	SCAN
rs1427785	WSCD2	cis	parietal	SCAN
rs1427785	NUAK1	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106485400-106500800	Weak transcription	Lung	lung
2	chr12:106485600-106500600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:106491200-106500800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:106492000-106504400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:106492600-106500600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:106492600-106500800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:106492800-106500600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:106493400-106512400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:106494400-106500800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:106495200-106500800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:106495200-106500800	Weak transcription	Gastric	stomach
12	chr12:106495600-106507200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:106496200-106500600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:106497200-106500600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:106497200-106501200	Weak transcription	Right Ventricle	heart
16	chr12:106497600-106500600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:106498000-106500800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:106498400-106500600	Weak transcription	Left Ventricle	heart
19	chr12:106498400-106507200	Weak transcription	Pancreas	Pancrea
20	chr12:106498600-106500600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:106499200-106502000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:106499400-106500800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:106499400-106503800	Enhancers	Brain Germinal Matrix	brain
24	chr12:106499400-106504000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:106499400-106505400	Enhancers	Fetal Intestine Small	intestine
26	chr12:106499600-106500800	Genic enhancers	HSMMtube	muscle
27	chr12:106499600-106502000	Flanking Active TSS	Fetal Heart	heart
28	chr12:106499600-106502800	Enhancers	Colon Smooth Muscle	Colon
29	chr12:106499600-106503000	Enhancers	Fetal Kidney	kidney
30	chr12:106499600-106503000	Enhancers	Ovary	ovary
31	chr12:106499600-106503200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:106499600-106503200	Enhancers	Fetal Muscle Leg	muscle
33	chr12:106499600-106503400	Enhancers	Psoas Muscle	Psoas
34	chr12:106499600-106503600	Enhancers	Brain Anterior Caudate	brain
35	chr12:106499600-106503600	Enhancers	Hela-S3	cervix
36	chr12:106499600-106503800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:106499600-106504200	Enhancers	Fetal Brain Male	brain
38	chr12:106499600-106504600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:106499600-106505000	Enhancers	Fetal Intestine Large	intestine
40	chr12:106499600-106505000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr12:106499600-106505200	Enhancers	Brain Cingulate Gyrus	brain
42	chr12:106499600-106511400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:106499800-106500600	Weak transcription	Right Atrium	heart
44	chr12:106499800-106500800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:106499800-106500800	Enhancers	Fetal Brain Female	brain
46	chr12:106499800-106501000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr12:106499800-106501200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:106499800-106501800	Enhancers	Stomach Smooth Muscle	stomach
49	chr12:106499800-106503200	Enhancers	NH-A	brain
50	chr12:106499800-106507800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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