Variant report

Variant	rs12555128
Chromosome Location	chr9:97681491-97681492
allele	C/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	MAX	chr9:97681372-97685528	A549	lung:	n/a	n/a
2	SP1	chr9:97681342-97685519	A549	lung:	n/a	n/a
3	EP300	chr9:97681350-97683738	A549	lung:	n/a	chr9:97683352-97683366 chr9:97683353-97683367 chr9:97683357-97683371 chr9:97682882-97682896
4	EGR1	chr9:97681426-97682467	MCF-7	breast:	n/a	chr9:97681698-97681712 chr9:97681700-97681710 chr9:97681754-97681767 chr9:97681699-97681712 chr9:97681700-97681711 chr9:97681700-97681711 chr9:97681694-97681716 chr9:97681700-97681710
5	SP1	chr9:97681324-97685508	A549	lung:	n/a	n/a
6	ATF3	chr9:97681482-97682389	A549	lung:	n/a	n/a
7	GATA3	chr9:97681311-97685467	A549	lung:	n/a	n/a
8	GATA3	chr9:97681437-97682720	MCF-7	breast:	n/a	n/a
9	TCF12	chr9:97681294-97685653	A549	lung:	n/a	chr9:97685588-97685595
10	SIN3AK20	chr9:97681417-97682677	MCF-7	breast:	n/a	n/a
11	MAX	chr9:97681433-97682475	A549	lung:	n/a	n/a
12	E2F6	chr9:97681426-97682448	A549	lung:	n/a	n/a
13	BCL3	chr9:97681414-97683736	A549	lung:	n/a	n/a
14	CEBPB	chr9:97681425-97682498	A549	lung:	n/a	n/a
15	EP300	chr9:97681469-97685519	A549	lung:	n/a	chr9:97683352-97683366 chr9:97683353-97683367 chr9:97683357-97683371 chr9:97682882-97682896

No.	Distal block	Cell Line	Cell type
1	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
2	chr9:97679968..97683217-chr9:97810510..97812408,3	MCF-7	breast:
3	chr9:97572097..97590438-chr9:97672990..97690806,63	MCF-7	breast:
4	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
5	chr9:97678927..97686235-chr9:97889117..97896057,11	MCF-7	breast:
6	chr9:97558473..97564935-chr9:97678907..97687123,11	MCF-7	breast:
7	chr9:97626847..97629665-chr9:97678256..97681885,4	MCF-7	breast:
8	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:
9	chr9:97654777..97656689-chr9:97679645..97682219,2	MCF-7	breast:
10	chr9:97646214..97649715-chr9:97676410..97681725,5	MCF-7	breast:
11	chr9:97661005..97662804-chr9:97680216..97681941,2	MCF-7	breast:
12	chr9:97661771..97663867-chr9:97680073..97682444,2	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000230815	Chromatin interaction
ENSG00000236095	Chromatin interaction
ENSG00000252153	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1020962	1.00[JPT][hapmap]
rs10217441	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1038092	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs10761362	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10761371	1.00[JPT][hapmap]
rs10993471	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs12552838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12553869	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12554043	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs12554454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12555829	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1382411	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1382412	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1530331	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs1542107	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs1564235	1.00[JPT][hapmap]
rs1571896	1.00[JPT][hapmap]
rs16911834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16911862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1871220	1.00[JPT][hapmap]
rs1888944	1.00[JPT][hapmap]
rs2026399	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2061798	1.00[JPT][hapmap]
rs2061801	1.00[JPT][hapmap]
rs2095069	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2104888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165715	1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs2306207	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2406898	1.00[TSI][hapmap]
rs2584805	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs35322834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356133	1.00[AFR][1000 genomes]
rs356145	1.00[AFR][1000 genomes]
rs356147	1.00[AFR][1000 genomes]
rs356148	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs3739748	1.00[JPT][hapmap]
rs3780560	1.00[JPT][hapmap]
rs3886568	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs3887267	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs41316526	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438742	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs456276	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes]
rs4743975	1.00[JPT][hapmap]
rs4743977	1.00[JPT][hapmap]
rs4743989	1.00[JPT][hapmap]
rs4744421	1.00[JPT][hapmap]
rs4744437	1.00[JPT][hapmap]
rs4744440	1.00[JPT][hapmap]
rs555799	1.00[AFR][1000 genomes]
rs56198429	1.00[AFR][1000 genomes]
rs56317174	1.00[AFR][1000 genomes]
rs6479578	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs66642068	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66863985	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67756624	0.90[AMR][1000 genomes]
rs7019602	1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs7022963	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7029570	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7035166	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7038891	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs7046900	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs72747019	1.00[AFR][1000 genomes]
rs72748596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748601	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750335	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72750346	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73538177	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7867856	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs7869736	1.00[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97661600-97686200	Weak transcription	Primary T cells from cord blood	blood
3	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:97671000-97684200	Weak transcription	Small Intestine	intestine
5	chr9:97671600-97681600	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:97673000-97681600	Weak transcription	Spleen	Spleen
7	chr9:97674200-97681600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:97674200-97681600	Enhancers	Placenta	Placenta
9	chr9:97675000-97684400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:97675200-97681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:97675400-97684000	Weak transcription	Psoas Muscle	Psoas
12	chr9:97676600-97683000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:97676600-97684200	Weak transcription	Colonic Mucosa	Colon
14	chr9:97676800-97683400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:97677000-97684000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:97677200-97681600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:97677200-97681600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:97677200-97682000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:97677200-97682000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:97677200-97682600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:97677200-97682600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:97677400-97681600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:97677400-97681600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:97677400-97681600	Weak transcription	NH-A	brain
25	chr9:97677400-97681600	Enhancers	NHEK	skin
26	chr9:97677400-97681600	Weak transcription	Osteobl	bone
27	chr9:97677400-97688600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:97678000-97681600	Weak transcription	NHLF	lung
29	chr9:97678000-97682600	Weak transcription	Brain Germinal Matrix	brain
30	chr9:97678000-97683000	Weak transcription	Fetal Intestine Large	intestine
31	chr9:97678000-97684400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:97678200-97681600	Weak transcription	Fetal Stomach	stomach
33	chr9:97678200-97681600	Weak transcription	Left Ventricle	heart
34	chr9:97678200-97681600	Weak transcription	HSMM	muscle
35	chr9:97678200-97682600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:97679000-97686400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr9:97679200-97683200	Enhancers	Stomach Mucosa	stomach
38	chr9:97679200-97687200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr9:97679400-97681600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:97679400-97687000	Enhancers	Fetal Heart	heart
41	chr9:97679600-97682800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:97679600-97682800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr9:97679800-97681600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr9:97679800-97681600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr9:97679800-97681600	Weak transcription	HMEC	breast
46	chr9:97679800-97681800	Weak transcription	Fetal Lung	lung
47	chr9:97679800-97682000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr9:97679800-97682000	Weak transcription	Brain Angular Gyrus	brain
49	chr9:97679800-97682000	Weak transcription	Brain Anterior Caudate	brain
50	chr9:97679800-97682000	Weak transcription	Fetal Kidney	kidney

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