Variant report

Variant	rs11525539
Chromosome Location	chr12:32963212-32963213
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	chr12:32962332..32964865-chr12:32975900..32977825,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057294	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10772002	0.88[ASN][1000 genomes]
rs10772003	0.90[ASN][1000 genomes]
rs10844355	0.88[ASN][1000 genomes]
rs10844356	0.88[ASN][1000 genomes]
rs10844357	0.88[ASN][1000 genomes]
rs10844358	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10844360	0.88[ASN][1000 genomes]
rs10844361	0.90[ASN][1000 genomes]
rs10844362	0.89[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs10844365	0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs10844367	0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs11052236	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11052247	0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11052249	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs11052250	0.89[ASN][1000 genomes]
rs11052251	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs11052252	0.90[ASN][1000 genomes]
rs11052253	0.90[ASN][1000 genomes]
rs11052255	0.90[ASN][1000 genomes]
rs11052261	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11533495	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11534764	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11534765	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs11561218	0.90[ASN][1000 genomes]
rs12228193	0.85[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs12231019	0.83[ASN][1000 genomes]
rs12299188	0.88[ASN][1000 genomes]
rs12299276	0.89[ASN][1000 genomes]
rs12580216	0.89[ASN][1000 genomes]
rs2389109	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs3789978	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs3850972	0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs3850973	0.88[ASN][1000 genomes]
rs3850974	0.88[ASN][1000 genomes]
rs3907042	0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4931038	0.83[ASN][1000 genomes]
rs56798911	0.88[ASN][1000 genomes]
rs59748919	0.84[ASN][1000 genomes]
rs7133291	0.90[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7138787	0.86[ASN][1000 genomes]
rs7302586	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs73301721	0.88[ASN][1000 genomes]
rs73301724	0.88[ASN][1000 genomes]
rs73301773	0.90[ASN][1000 genomes]
rs7960291	0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7963034	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7974049	0.80[ASN][1000 genomes]
rs7975210	0.85[ASN][1000 genomes]
rs9988940	0.90[ASN][1000 genomes]
rs9988941	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs9988988	0.90[ASN][1000 genomes]
rs9989018	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv532334	chr12:32884789-33034791	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3409346	chr12:32962935-32964933	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3428961	chr12:32963198-32963982	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32941800-33033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:32943800-33026800	Weak transcription	Fetal Kidney	kidney
3	chr12:32944200-32989400	Weak transcription	Hela-S3	cervix
4	chr12:32945800-32972400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:32946000-32973600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:32946600-32967200	Weak transcription	Stomach Mucosa	stomach
7	chr12:32949200-32975200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:32949200-32987000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:32949200-33007800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:32954200-32963400	Weak transcription	HMEC	breast
11	chr12:32954400-32968800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:32959000-32965000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:32960200-32969200	Weak transcription	Small Intestine	intestine
14	chr12:32960800-32965400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr12:32961000-32989800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:32961400-32965200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr12:32961400-32969400	Strong transcription	NHEK	skin
18	chr12:32961400-32971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:32961600-32963600	Enhancers	HSMMtube	muscle
20	chr12:32961600-32965200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr12:32961800-32973400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:32961800-32974800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:32962000-32964400	Strong transcription	Fetal Intestine Large	intestine
24	chr12:32962000-32965000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:32962000-32965400	Strong transcription	Liver	Liver
26	chr12:32962000-32973600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:32962200-32965400	Enhancers	Brain Cingulate Gyrus	brain
28	chr12:32962200-32969200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:32962200-32974000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:32962400-32963600	Enhancers	Left Ventricle	heart
31	chr12:32962400-32964600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:32962400-32970600	Weak transcription	Fetal Stomach	stomach
33	chr12:32962400-32973400	Weak transcription	Gastric	stomach
34	chr12:32962400-32973400	Weak transcription	Right Atrium	heart
35	chr12:32962600-32965000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:32962600-32965000	Enhancers	Brain Hippocampus Middle	brain
37	chr12:32962600-32973400	Weak transcription	Pancreas	Pancrea
38	chr12:32962800-32963600	Enhancers	Brain Angular Gyrus	brain
39	chr12:32962800-32963600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:32962800-32964200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:32962800-32967000	Weak transcription	Right Ventricle	heart
42	chr12:32963000-32963600	Flanking Active TSS	Fetal Heart	heart
43	chr12:32963000-32963800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:32963000-32963800	Weak transcription	HepG2	liver
45	chr12:32963000-32964000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:32963000-32968200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr12:32963000-32970600	Weak transcription	Fetal Intestine Small	intestine
48	chr12:32963000-32986800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:32963200-32963400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
50	chr12:32963200-32964000	Weak transcription	Colonic Mucosa	Colon

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