Variant report

Variant	rs55969660
Chromosome Location	chr15:73343331-73343332
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr15:73342653-73346307	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:73075212..73078087-chr15:73342810..73345457,4	MCF-7	breast:
2	chr15:72765203..72766825-chr15:73342381..73345092,2	MCF-7	breast:
3	chr15:73074691..73078350-chr15:73341676..73346479,5	MCF-7	breast:

Variant related genes	Relation type
NEO1	TF binding region
ENSG00000261423	Chromatin interaction
ENSG00000159322	Chromatin interaction
ENSG00000260898	Chromatin interaction
ENSG00000166233	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1017809	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1029	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1038136	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11852881	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11853109	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856383	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856433	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856466	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11857053	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12101540	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12101734	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13329282	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1382780	0.88[EUR][1000 genomes]
rs1678245	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16957661	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1714529	0.88[EUR][1000 genomes]
rs1714530	0.88[EUR][1000 genomes]
rs1714532	0.88[EUR][1000 genomes]
rs1812363	0.88[EUR][1000 genomes]
rs1842164	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1963253	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1963254	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1979410	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2169952	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254390	0.85[EUR][1000 genomes]
rs2254818	0.85[EUR][1000 genomes]
rs2623990	0.85[EUR][1000 genomes]
rs2623996	0.88[EUR][1000 genomes]
rs2680347	0.88[EUR][1000 genomes]
rs2680348	0.82[EUR][1000 genomes]
rs2680351	0.88[EUR][1000 genomes]
rs28547177	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28572029	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28582318	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28645758	0.80[EUR][1000 genomes]
rs28676873	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28808999	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28828370	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4238459	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4287530	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4325518	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4539561	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4635304	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4776626	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4777584	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57453823	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6495054	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176908	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7180017	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438015	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7403367	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7497831	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031718	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8034243	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8035499	0.91[EUR][1000 genomes]
rs8035717	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8038411	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs899480	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920152	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920459	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920675	0.88[AMR][1000 genomes];0.88[EUR][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	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73339200-73343400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:73339400-73343600	Weak transcription	Pancreas	Pancrea
3	chr15:73341600-73343400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr15:73341600-73343400	Enhancers	Brain Cingulate Gyrus	brain
5	chr15:73341800-73343400	Enhancers	Brain Hippocampus Middle	brain
6	chr15:73342000-73343600	Weak transcription	Fetal Stomach	stomach
7	chr15:73342200-73343400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:73342400-73343400	Enhancers	Brain Angular Gyrus	brain
9	chr15:73342600-73343400	Weak transcription	Brain Substantia Nigra	brain
10	chr15:73342600-73343600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:73343000-73343400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:73343000-73343400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr15:73343000-73346000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr15:73343200-73343400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr15:73343200-73343400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
16	chr15:73343200-73343400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
17	chr15:73343200-73343400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
18	chr15:73343200-73343400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr15:73343200-73343400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:73343200-73343400	Enhancers	Liver	Liver
21	chr15:73343200-73343400	Enhancers	Brain Germinal Matrix	brain
22	chr15:73343200-73343400	Enhancers	Colon Smooth Muscle	Colon
23	chr15:73343200-73343400	Enhancers	Fetal Brain Male	brain
24	chr15:73343200-73343400	Enhancers	Fetal Intestine Small	intestine
25	chr15:73343200-73343400	Enhancers	Fetal Kidney	kidney
26	chr15:73343200-73343400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:73343200-73343400	Enhancers	A549	lung
28	chr15:73343200-73343600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:73343200-73343600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr15:73343200-73343600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:73343200-73343600	Flanking Active TSS	Fetal Brain Female	brain
32	chr15:73343200-73343600	Enhancers	Fetal Heart	heart
33	chr15:73343200-73343600	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr15:73343200-73343600	Enhancers	Rectal Smooth Muscle	rectum
35	chr15:73343200-73343600	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr15:73343200-73343600	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr15:73343200-73343800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:73343200-73343800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:73343200-73343800	Flanking Active TSS	Fetal Lung	lung
40	chr15:73343200-73343800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr15:73343200-73344000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:73343200-73345800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr15:73343200-73346000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr15:73343200-73346000	Active TSS	Brain Anterior Caudate	brain
45	chr15:73343200-73346200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr15:73343200-73346400	Active TSS	H1 Cell Line	embryonic stem cell
47	chr15:73343200-73346400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:73343200-73346400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:73343200-73346600	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr15:73343200-73347600	Active TSS	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links