Variant report

Variant	rs1635536
Chromosome Location	chr12:48385945-48385946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48373823..48376376-chr12:48383731..48387007,3	MCF-7	breast:
2	chr12:48384703..48387276-chr12:48389834..48391406,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1034762	0.93[EUR][1000 genomes]
rs1621710	0.92[ASN][1000 genomes]
rs1635526	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1635528	0.81[AMR][1000 genomes]
rs1635529	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1635534	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635535	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635537	0.86[ASN][1000 genomes]
rs1635544	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1635546	0.82[ASN][1000 genomes]
rs1635547	0.82[ASN][1000 genomes]
rs1635550	0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs1793911	0.92[ASN][1000 genomes]
rs1793912	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1793913	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1793915	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1793917	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793923	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1793924	0.92[ASN][1000 genomes]
rs1793931	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1793933	0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1793955	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1793956	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs740024	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs917055	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1635536	ZNF641	cis	Whole Blood	GTEx
rs1635536	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48381400-48386400	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:48381400-48386800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48381400-48388800	Weak transcription	Fetal Intestine Small	intestine
5	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:48383000-48388400	Weak transcription	Psoas Muscle	Psoas
7	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48384000-48386000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr12:48384200-48387600	Enhancers	Fetal Lung	lung
11	chr12:48384400-48386200	Enhancers	Fetal Brain Female	brain
12	chr12:48384400-48386400	Enhancers	Fetal Brain Male	brain
13	chr12:48384400-48386600	Bivalent Enhancer	Fetal Stomach	stomach
14	chr12:48384600-48386000	Enhancers	Placenta	Placenta
15	chr12:48384600-48386400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:48384600-48386400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:48384800-48386200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:48384800-48386200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:48385000-48386000	Enhancers	Right Ventricle	heart
20	chr12:48385200-48386000	Enhancers	Brain Germinal Matrix	brain
21	chr12:48385200-48391600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:48385400-48386200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:48385400-48386400	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr12:48385600-48389000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:48385600-48389600	Weak transcription	Right Atrium	heart
26	chr12:48385800-48387400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:48385800-48387400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:48385800-48389600	Weak transcription	Left Ventricle	heart
29	chr12:48385800-48389600	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links