Variant report

Variant	rs10962260
Chromosome Location	chr9:16039883-16039884
allele	G/T
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	TCF12	chr9:16039078-16040996	ECC-1	luminal epithelium:	n/a	chr9:16040102-16040109 chr9:16040100-16040110
2	FOXM1	chr9:16039743-16041030	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr9:16039241-16040735	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr9:16039091-16040868	ECC-1	luminal epithelium:	n/a	chr9:16039302-16039312
5	GATA3	chr9:16039740-16040046	SH-SY5Y	brain:	n/a	n/a
6	MYC	chr9:16039292-16039884	NB4	blood:	n/a	chr9:16039302-16039312
7	NFIC	chr9:16039074-16040990	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr9:16039029-16041411	ECC-1	luminal epithelium:	n/a	chr9:16039302-16039312
9	YY1	chr9:16039291-16040040	H1-hESC	embryonic stem cell:	n/a	n/a
10	EP300	chr9:16039015-16041060	ECC-1	luminal epithelium:	n/a	chr9:16040874-16040888
11	YY1	chr9:16039198-16040708	ECC-1	luminal epithelium:	n/a	n/a
12	YY1	chr9:16039693-16039953	GM12878	blood:	n/a	n/a
13	YY1	chr9:16039617-16039947	GM12892	blood:	n/a	n/a
14	NFIC	chr9:16039069-16040974	ECC-1	luminal epithelium:	n/a	n/a
15	YY1	chr9:16039677-16039954	GM12878	blood:	n/a	n/a
16	TEAD4	chr9:16039101-16040970	ECC-1	luminal epithelium:	n/a	n/a
17	TCF12	chr9:16039121-16040912	ECC-1	luminal epithelium:	n/a	chr9:16040102-16040109 chr9:16040100-16040110
18	YY1	chr9:16039642-16039945	GM12892	blood:	n/a	n/a
19	CTCF	chr9:16039800-16039950	GM12875	blood:	n/a	n/a
20	GATA2	chr9:16039756-16040487	SH-SY5Y	brain:	n/a	chr9:16040260-16040270 chr9:16040263-16040270

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:16039283..16040078-chr9:16131109..16131609,2	MCF-7	breast:

Variant related genes	Relation type
CCDC171	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1014307	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10733306	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10733307	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10738420	0.82[CEU][hapmap]
rs10738423	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10738424	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738425	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10738426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10738427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10738428	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10738430	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10756724	0.81[CEU][hapmap]
rs10756726	0.82[CEU][hapmap]
rs10756734	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756735	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10756736	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10756737	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10756738	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756739	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10756741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10756742	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10810485	0.83[CEU][hapmap]
rs10810517	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810518	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10810519	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10810520	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10810521	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10810522	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10810523	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10810524	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10810526	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10810527	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810528	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11788695	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12379466	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1328273	0.88[EUR][1000 genomes]
rs1328274	0.88[EUR][1000 genomes]
rs1328275	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1328276	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1328277	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1328278	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1328279	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1328280	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1328296	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1328298	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1359954	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1359956	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1359957	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1410444	0.83[CEU][hapmap]
rs1410450	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1410451	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1410452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1410453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1410454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1410455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1887666	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1887667	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1887668	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1887669	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2026661	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2149233	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2382551	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4247294	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4472620	0.82[CEU][hapmap]
rs4740631	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4740632	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4741557	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4741558	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4741559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4741560	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4741561	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7040690	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752489	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs752490	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7873925	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943787	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs943788	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs943789	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs961117	0.83[CEU][hapmap]
rs9792412	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs997410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025555	chr9:16022186-16064158	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16023600-16040600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:16030800-16050000	Weak transcription	Aorta	Aorta
3	chr9:16034000-16043600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:16039000-16041400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr9:16039000-16041400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:16039000-16041400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:16039000-16041400	Enhancers	Fetal Kidney	kidney
8	chr9:16039000-16041400	Enhancers	Rectal Smooth Muscle	rectum
9	chr9:16039000-16041600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr9:16039000-16041600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr9:16039200-16040000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:16039200-16040000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:16039200-16040200	Enhancers	Stomach Smooth Muscle	stomach
14	chr9:16039200-16040600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:16039200-16040800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:16039200-16040800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr9:16039200-16041200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr9:16039200-16041400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr9:16039200-16041400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:16039200-16041400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:16039200-16041400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:16039200-16041400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:16039200-16041400	Enhancers	Fetal Lung	lung
24	chr9:16039200-16041400	Enhancers	Ovary	ovary
25	chr9:16039200-16041400	Enhancers	NH-A	brain
26	chr9:16039200-16041600	Enhancers	Fetal Muscle Leg	muscle
27	chr9:16039200-16042800	Enhancers	Fetal Stomach	stomach
28	chr9:16039400-16040200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:16039400-16040400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:16039400-16041000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr9:16039400-16041400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:16039600-16041200	Enhancers	Colon Smooth Muscle	Colon
33	chr9:16039600-16042400	Enhancers	Adipose Nuclei	Adipose
34	chr9:16039800-16040400	Enhancers	H9 Cell Line	embryonic stem cell
35	chr9:16039800-16040400	Enhancers	Fetal Heart	heart
36	chr9:16039800-16040600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:16039800-16040600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:16039800-16040600	Enhancers	Fetal Muscle Trunk	muscle
39	chr9:16039800-16042600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:16039800-16043400	Weak transcription	Osteobl	bone

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