Variant report

Variant	rs12595434
Chromosome Location	chr15:73343236-73343237
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	GATA3	chr15:73342583-73343273	SH-SY5Y	brain:	n/a	chr15:73343036-73343047
2	MXI1	chr15:73342653-73346307	SK-N-SH	brain:	n/a	n/a
3	TBP	chr15:73343235-73343281	GM12878	blood:	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
ENSG00000260898	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000159322	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1017808	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs11072405	0.86[CHB][hapmap]
rs1119251	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs11634045	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs11636981	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11856537	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12594776	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs12901649	0.85[CHB][hapmap]
rs13379710	0.83[ASN][1000 genomes]
rs1382782	0.86[CEU][hapmap];0.91[CHB][hapmap]
rs1564347	0.86[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes]
rs1585766	0.82[CHB][hapmap]
rs16957683	0.82[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2415145	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs28742992	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4436752	0.83[ASN][1000 genomes]
rs4776623	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4777585	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4777587	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4777588	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777592	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes]
rs6495044	0.82[ASN][1000 genomes]
rs6495045	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495046	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495050	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495051	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495052	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6495053	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6495057	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495058	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7163543	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7168555	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7173710	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7177758	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7178123	0.81[ASN][1000 genomes]
rs7184025	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7495084	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8039418	0.82[CHB][hapmap]
rs9806269	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	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

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